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Weadick CS, Goggin C, Keogh RJ, Murphy JF, Feeley L, Bennett MW, O’Reilly S, Redmond HP, Kelly J, O’Mahony D, Noonan S, Clover AJP, Bambury RM. Risk Stratification Tools to Aid Decisions on Adjuvant Chemotherapy Usage in Resected Soft Tissue Sarcomas: A Ten-Year Review of an Irish Sarcoma Center Experience. World J Oncol 2024; 15:640-647. [PMID: 38993253 PMCID: PMC11236376 DOI: 10.14740/wjon1863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/01/2024] [Indexed: 07/13/2024] Open
Abstract
Background Soft tissue sarcoma (STS) is comprised of approximately 80 subtypes, with an incidence of 4 - 5 per 100,000 annually in Europe. The National Comprehensive Cancer Network (NCCN) guidelines recommend consideration of neoadjuvant/adjuvant chemotherapy in tumors at high risk of recurrence based on the American Joint Committee on Cancer (AJCC) staging. Alternatively, the Sarculator is a risk prediction tool that has identified a threshold of risk, above which chemotherapy may provide an overall survival (OS) benefit. Using this nomogram, patients with a 10-year predicted OS < 60% are classified as high risk and should be considered for chemotherapy. The aim of this study was to assess the prognostic accuracy of these two risk prediction methods in an Irish population. Methods All newly diagnosed patients with resected STS discussed in the STS tumor board in Cork University Hospital between January 2012 and December 2021 were identified. Clinicopathological data were collected. Risk assessment using AJCC and Sarculator nomogram was performed on all patients with an extremity/trunk sarcoma. The OS was calculated including Kaplan-Meier method for time to event analysis. Results In total, 200 STS patients were reviewed, of whom 134 had truncal or extremity tumors. Sarculator score was calculated for 60 of these (well differentiated liposarcomas, desmoid tumors and dermatofibrosarcoma protuberans were excluded). Using the Sarculator nomogram to calculate 10-year predicted OS, 19 patients were categorized as high risk and 41 were categorized as low risk. Using AJCC staging, 25 patients were categorized as high risk and 35 as low risk. The 5-year OS rate in the Sarculator high-risk group was 60.2%, compared with 87.1% in the low-risk group (P = 0.009). The 5-year OS rate in the AJCC high-risk group was 67.6%, compared with 86.3% in the low-risk group (P = 0.083). Conclusions Our cohort is representative of the broad histological subtypes expected. In our population, Sarculator score results correlate with international outcomes and higher scores were associated with increased mortality. The Sarculator was more predictive of clinical outcome than AJCC staging, and its use would lower the proportion of patients being considered for adjuvant chemotherapy thereby sparing toxicity, which is important in the setting of uncertain clinical benefit.
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Affiliation(s)
| | - Caitriona Goggin
- Department of Medical Oncology, Cork University Hospital, Wilton, Cork, Ireland
| | - Rachel J. Keogh
- Department of Medical Oncology, Cork University Hospital, Wilton, Cork, Ireland
| | - Jake F. Murphy
- Department of Radiation Oncology, Cork University Hospital, Wilton, Cork, Ireland
| | - Linda Feeley
- Department of Histopathology, Cork University Hospital, Wilton, Cork, Ireland
| | - Michael W. Bennett
- Department of Histopathology, Cork University Hospital, Wilton, Cork, Ireland
| | - Seamus O’Reilly
- Department of Medical Oncology, Cork University Hospital, Wilton, Cork, Ireland
- Cancer Research @UCC, University College Cork, Cork, Ireland
| | - H. Paul Redmond
- Department of Surgery, Cork University Hospital, Wilton, Cork, Ireland
| | - Jason Kelly
- Department of Surgery, Cork University Hospital, Wilton, Cork, Ireland
| | - Deirdre O’Mahony
- Department of Medical Oncology, Cork University Hospital, Wilton, Cork, Ireland
| | - Sinead Noonan
- Department of Medical Oncology, Cork University Hospital, Wilton, Cork, Ireland
- Cancer Research @UCC, University College Cork, Cork, Ireland
| | - A. James P Clover
- Department of Plastic Surgery, Cork University Hospital, Wilton, Cork, Ireland
| | - Richard M. Bambury
- Department of Medical Oncology, Cork University Hospital, Wilton, Cork, Ireland
- Cancer Research @UCC, University College Cork, Cork, Ireland
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Nief CA, Hammer PM, Wang A, Charu V, Tanweer A, Litkouhi B, Kidd E, Gentles AJ, Howitt BE. Endometrioid Endometrial RNA Index Predicts Recurrence in Stage I Patients. Clin Cancer Res 2024; 30:2801-2811. [PMID: 38669067 DOI: 10.1158/1078-0432.ccr-23-3158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/13/2024] [Accepted: 04/24/2024] [Indexed: 07/02/2024]
Abstract
PURPOSE Risk prediction with genomic and transcriptomic data has the potential to improve patient outcomes by enabling clinicians to identify patients requiring adjuvant treatment approaches, while sparing low-risk patients from unnecessary interventions. Endometrioid endometrial carcinoma (EEC) is the most common cancer in women in developed countries, and rates of endometrial cancer are increasing. EXPERIMENTAL DESIGN We collected a 105-patient case-control cohort of stage I EEC comprising 45 patients who experienced recurrence less than 6 years after excision, and 60 Fédération Internationale de Gynécologie et d'Obstétrique grade-matched controls without recurrence. We first utilized two RNA-based, previously validated machine learning approaches, namely, EcoTyper and Complexity Index in Sarcoma (CINSARC). We developed Endometrioid Endometrial RNA Index (EERI), which uses RNA expression data from 46 genes to generate a personalized risk score for each patient. EERI was trained on our 105-patient cohort and tested on a publicly available cohort of 263 patients with stage I EEC. RESULTS EERI was able to predict recurrences with 94% accuracy in the training set and 81% accuracy in the test set. In the test set, patients assigned as EERI high-risk were significantly more likely to experience recurrence (30%) than the EERI low-risk group (1%) with a hazard ratio of 9.9 (95% CI, 4.1-23.8; P < 0.001). CONCLUSIONS Tumors with high-risk genetic features may require additional treatment or closer monitoring and are not readily identified using traditional clinicopathologic and molecular features. EERI performs with high sensitivity and modest specificity, which may benefit from further optimization and validation in larger independent cohorts.
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Affiliation(s)
- Corrine A Nief
- Stanford University School of Medicine, Stanford, California
- Department of Pathology, Stanford University, Stanford, California
| | - Phoebe M Hammer
- Department of Pathology, Stanford University, Stanford, California
| | - Aihui Wang
- Department of Pathology, Stanford University, Stanford, California
| | - Vivek Charu
- Department of Pathology, Stanford University, Stanford, California
| | - Amina Tanweer
- Department of Pathology, Stanford University, Stanford, California
| | - Babak Litkouhi
- Department of Biomedical Data Science, Stanford University, Stanford, California
| | - Elizabeth Kidd
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Andrew J Gentles
- Department of Pathology, Stanford University, Stanford, California
- Department of Gynecologic Oncology, Stanford University, Stanford, California
| | - Brooke E Howitt
- Department of Pathology, Stanford University, Stanford, California
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3
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Crombé A, Lucchesi C, Bertolo F, Kind M, Spalato-Ceruso M, Toulmonde M, Chaire V, Michot A, Coindre JM, Perret R, Le Loarer F, Bourdon A, Italiano A. Integration of pre-treatment computational radiomics, deep radiomics, and transcriptomics enhances soft-tissue sarcoma patient prognosis. NPJ Precis Oncol 2024; 8:129. [PMID: 38849448 PMCID: PMC11161510 DOI: 10.1038/s41698-024-00616-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/17/2024] [Indexed: 06/09/2024] Open
Abstract
Our objective was to capture subgroups of soft-tissue sarcoma (STS) using handcraft and deep radiomics approaches to understand their relationship with histopathology, gene-expression profiles, and metastatic relapse-free survival (MFS). We included all consecutive adults with newly diagnosed locally advanced STS (N = 225, 120 men, median age: 62 years) managed at our sarcoma reference center between 2008 and 2020, with contrast-enhanced baseline MRI. After MRI postprocessing, segmentation, and reproducibility assessment, 175 handcrafted radiomics features (h-RFs) were calculated. Convolutional autoencoder neural network (CAE) and half-supervised CAE (HSCAE) were trained in repeated cross-validation on representative contrast-enhanced slices to extract 1024 deep radiomics features (d-RFs). Gene-expression levels were calculated following RNA sequencing (RNAseq) of 110 untreated samples from the same cohort. Unsupervised classifications based on h-RFs, CAE, HSCAE, and RNAseq were built. The h-RFs, CAE, and HSCAE grouping were not associated with the transcriptomics groups but with prognostic radiological features known to correlate with lower survivals and higher grade and SARCULATOR groups (a validated prognostic clinical-histological nomogram). HSCAE and h-RF groups were also associated with MFS in multivariable Cox regressions. Combining HSCAE and transcriptomics groups significantly improved the prognostic performances compared to each group alone, according to the concordance index. The combined radiomic-transcriptomic group with worse MFS was characterized by the up-regulation of 707 genes and 292 genesets related to inflammation, hypoxia, apoptosis, and cell differentiation. Overall, subgroups of STS identified on pre-treatment MRI using handcrafted and deep radiomics were associated with meaningful clinical, histological, and radiological characteristics, and could strengthen the prognostic value of transcriptomics signatures.
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Affiliation(s)
- Amandine Crombé
- Department of Oncologic Imaging, Bergonié Institute, F-33076, Bordeaux, France.
- Department of Radiology, Pellegrin University Hospital, F-33076, Bordeaux, France.
- Bordeaux Institute of Oncology, BRIC U1312, Sarcotarget team, INSERM, University of Bordeaux, Institut Bergonié, F-33000, Bordeaux, France.
| | - Carlo Lucchesi
- Department of Bioinformatics, Bergonié Institute, F-33076, Bordeaux, France
| | - Frédéric Bertolo
- Department of Bioinformatics, Bergonié Institute, F-33076, Bordeaux, France
| | - Michèle Kind
- Department of Oncologic Imaging, Bergonié Institute, F-33076, Bordeaux, France
| | - Mariella Spalato-Ceruso
- Bordeaux Institute of Oncology, BRIC U1312, Sarcotarget team, INSERM, University of Bordeaux, Institut Bergonié, F-33000, Bordeaux, France
- Department of Medical Oncology, Bergonié Institute, F-33076, Bordeaux, France
| | - Maud Toulmonde
- Bordeaux Institute of Oncology, BRIC U1312, Sarcotarget team, INSERM, University of Bordeaux, Institut Bergonié, F-33000, Bordeaux, France
- Department of Medical Oncology, Bergonié Institute, F-33076, Bordeaux, France
| | - Vanessa Chaire
- Bordeaux Institute of Oncology, BRIC U1312, Sarcotarget team, INSERM, University of Bordeaux, Institut Bergonié, F-33000, Bordeaux, France
- Department of Pathology, Bergonié Institute, F-33076, Bordeaux, France
| | - Audrey Michot
- Bordeaux Institute of Oncology, BRIC U1312, Sarcotarget team, INSERM, University of Bordeaux, Institut Bergonié, F-33000, Bordeaux, France
- Department of Oncologic Surgery, Bergonié Institute, F-33076, Bordeaux, France
| | - Jean-Michel Coindre
- Bordeaux Institute of Oncology, BRIC U1312, Sarcotarget team, INSERM, University of Bordeaux, Institut Bergonié, F-33000, Bordeaux, France
- Department of Pathology, Bergonié Institute, F-33076, Bordeaux, France
| | - Raul Perret
- Department of Pathology, Bergonié Institute, F-33076, Bordeaux, France
| | - François Le Loarer
- Bordeaux Institute of Oncology, BRIC U1312, Sarcotarget team, INSERM, University of Bordeaux, Institut Bergonié, F-33000, Bordeaux, France
- Department of Pathology, Bergonié Institute, F-33076, Bordeaux, France
| | - Aurélien Bourdon
- Department of Bioinformatics, Bergonié Institute, F-33076, Bordeaux, France
| | - Antoine Italiano
- Bordeaux Institute of Oncology, BRIC U1312, Sarcotarget team, INSERM, University of Bordeaux, Institut Bergonié, F-33000, Bordeaux, France
- Department of Medical Oncology, Bergonié Institute, F-33076, Bordeaux, France
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Liu J, Moura DS, Jones RL, Aggarwal A, Ebert PJ, Wagner AJ, Wright J, Martin-Broto J, Tap WD. Best Overall Response-Associated Signature to Doxorubicin in Soft Tissue Sarcomas: A Transcriptomic Analysis from ANNOUNCE. Clin Cancer Res 2024; 30:2598-2608. [PMID: 38536068 DOI: 10.1158/1078-0432.ccr-23-3936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/23/2024] [Accepted: 03/22/2024] [Indexed: 06/04/2024]
Abstract
PURPOSE This exploratory analysis evaluated the tumor samples of the patients treated with doxorubicin (with or without olaratumab) in a negative phase III ANNOUNCE trial to better understand the complexity of advanced soft tissue sarcomas (STS) and to potentially identify its predictive markers. EXPERIMENTAL DESIGN RNA sequencing was performed on pretreatment tumor samples (n = 273) from the ANNOUNCE trial to evaluate response patterns and identify potential predictive treatment markers for doxorubicin. A BOR-associated signature to doxorubicin (REDSARC) was created by evaluating tumors with radiographic response versus progression. An external cohort of doxorubicin-treated patients from the Spanish Group for Research on Sarcomas (GEIS) was used for refinement and validation. RESULTS A total of 259 samples from the trial were considered for analysis. Comparative analyses by the treatment arm did not explain the negative trial. However, there was an association between the BOR signature and histologic subtype (χ2P = 2.0e-7) and grade (P = 0.002). There were no associations between the BOR signature and gender, age, ethnicity, or stage. Applied to survival outcomes, REDSARC was also predictive for progression-free survival (PFS) and overall survival (OS). Using the GEIS cohort, a refined 25-gene signature was identified and applied to the ANNOUNCE cohort, where it was predictive of PFS and OS in leiomyosarcoma, liposarcoma, and other sarcoma subtypes, but not in undifferentiated pleomorphic sarcoma. CONCLUSIONS The refined REDSARC signature provides a potential tool to direct the application of doxorubicin in sarcomas and other malignancies. Validation and further refinement of the signature in other potentially subtype specific prospective cohorts is recommended.
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Affiliation(s)
| | - David S Moura
- Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Robin L Jones
- Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | | | | | | | | | - Javier Martin-Broto
- Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - William D Tap
- Memorial Sloan Kettering Cancer Center, New York, New York
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Marugán C, Sanz‐Gómez N, Ortigosa B, Monfort‐Vengut A, Bertinetti C, Teijo A, González M, Alonso de la Vega A, Lallena MJ, Moreno‐Bueno G, de Cárcer G. TPX2 overexpression promotes sensitivity to dasatinib in breast cancer by activating YAP transcriptional signaling. Mol Oncol 2024; 18:1531-1551. [PMID: 38357786 PMCID: PMC11161735 DOI: 10.1002/1878-0261.13602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/03/2024] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
Chromosomal instability (CIN) is a hallmark of cancer aggressiveness, providing genetic plasticity and tumor heterogeneity that allows the tumor to evolve and adapt to stress conditions. CIN is considered a cancer therapeutic biomarker because healthy cells do not exhibit CIN. Despite recent efforts to identify therapeutic strategies related to CIN, the results obtained have been very limited. CIN is characterized by a genetic signature where a collection of genes, mostly mitotic regulators, are overexpressed in CIN-positive tumors, providing aggressiveness and poor prognosis. We attempted to identify new therapeutic strategies related to CIN genes by performing a drug screen, using cells that individually express CIN-associated genes in an inducible manner. We find that the overexpression of targeting protein for Xklp2 (TPX2) enhances sensitivity to the proto-oncogene c-Src (SRC) inhibitor dasatinib due to activation of the Yes-associated protein 1 (YAP) pathway. Furthermore, using breast cancer data from The Cancer Genome Atlas (TCGA) and a cohort of cancer-derived patient samples, we find that both TPX2 overexpression and YAP activation are present in a significant percentage of cancer tumor samples and are associated with poor prognosis; therefore, they are putative biomarkers for selection for dasatinib therapy.
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Grants
- 2018-20I114 Spanish National Research Council (CSIC)
- 2021-AEP035 Spanish National Research Council (CSIC)
- 2022-20I018 Spanish National Research Council (CSIC)
- FJC2020-044620-I Ministerio de Ciencia, Innovación, Agencia Estatal de Investigación MCIN/AEI/FEDER
- PID2019-104644RB-I00 Ministerio de Ciencia, Innovación, Agencia Estatal de Investigación MCIN/AEI/FEDER
- PID2021-125705OB-I00 Ministerio de Ciencia, Innovación, Agencia Estatal de Investigación MCIN/AEI/FEDER
- PID2022-136854OB-I00 Ministerio de Ciencia, Innovación, Agencia Estatal de Investigación MCIN/AEI/FEDER
- RTI2018-095496-B-I00 Ministerio de Ciencia, Innovación, Agencia Estatal de Investigación MCIN/AEI/FEDER
- CB16/12/00295 Instituto de Salud Carlos III - CIBERONC
- LABAE16017DECA Spanish Association Against Cancer (AECC) Scientific Foundation
- POSTD234371SANZ Spanish Association Against Cancer (AECC) Scientific Foundation
- PROYE19036MOR Spanish Association Against Cancer (AECC) Scientific Foundation
- Spanish National Research Council (CSIC)
- Spanish Association Against Cancer (AECC) Scientific Foundation
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Affiliation(s)
- Carlos Marugán
- Cell Cycle & Cancer Biomarkers Laboratory, Cancer DepartmentInstituto de Investigaciones Biomédicas Sols‐Morreale (IIBM) CSIC‐UAMMadridSpain
- Discovery Chemistry Research and TechnologyEli Lilly and CompanyMadridSpain
| | - Natalia Sanz‐Gómez
- Cell Cycle & Cancer Biomarkers Laboratory, Cancer DepartmentInstituto de Investigaciones Biomédicas Sols‐Morreale (IIBM) CSIC‐UAMMadridSpain
| | - Beatriz Ortigosa
- Cell Cycle & Cancer Biomarkers Laboratory, Cancer DepartmentInstituto de Investigaciones Biomédicas Sols‐Morreale (IIBM) CSIC‐UAMMadridSpain
- Translational Cancer Research Laboratory, Cancer DepartmentInstituto de Investigaciones Biomédicas Alberto Sols‐Morreale (IIBM) CSIC‐UAMMadridSpain
| | - Ana Monfort‐Vengut
- Cell Cycle & Cancer Biomarkers Laboratory, Cancer DepartmentInstituto de Investigaciones Biomédicas Sols‐Morreale (IIBM) CSIC‐UAMMadridSpain
| | - Cristina Bertinetti
- Cell Cycle & Cancer Biomarkers Laboratory, Cancer DepartmentInstituto de Investigaciones Biomédicas Sols‐Morreale (IIBM) CSIC‐UAMMadridSpain
| | - Ana Teijo
- Pathology DepartmentMD Anderson Cancer CenterMadridSpain
| | - Marta González
- Cell Cycle & Cancer Biomarkers Laboratory, Cancer DepartmentInstituto de Investigaciones Biomédicas Sols‐Morreale (IIBM) CSIC‐UAMMadridSpain
| | - Alicia Alonso de la Vega
- Cell Cycle & Cancer Biomarkers Laboratory, Cancer DepartmentInstituto de Investigaciones Biomédicas Sols‐Morreale (IIBM) CSIC‐UAMMadridSpain
| | - María José Lallena
- Discovery Chemistry Research and TechnologyEli Lilly and CompanyMadridSpain
| | - Gema Moreno‐Bueno
- Translational Cancer Research Laboratory, Cancer DepartmentInstituto de Investigaciones Biomédicas Alberto Sols‐Morreale (IIBM) CSIC‐UAMMadridSpain
- MD Anderson International FoundationMadridSpain
- Biomedical Cancer Research Network (CIBERONC)MadridSpain
- CSIC Conexión‐Cáncer Hub (https://conexion‐cancer.csic.es)
| | - Guillermo de Cárcer
- Cell Cycle & Cancer Biomarkers Laboratory, Cancer DepartmentInstituto de Investigaciones Biomédicas Sols‐Morreale (IIBM) CSIC‐UAMMadridSpain
- CSIC Conexión‐Cáncer Hub (https://conexion‐cancer.csic.es)
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Czarnecka AM, Chmiel P, Błoński P, Rutkowski P. Establishing biomarkers for soft tissue sarcomas. Expert Rev Anticancer Ther 2024; 24:407-421. [PMID: 38682679 DOI: 10.1080/14737140.2024.2346187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 04/18/2024] [Indexed: 05/01/2024]
Abstract
INTRODUCTION Soft tissue sarcomas (STS) are a rare and diverse group of tumors. Curative options are limited to localized disease, with surgery being the mainstay. Advanced stages are associated with a poor prognosis. Currently, the prognosis of the patient is based on histological classification and clinical characteristics, with only a few biomarkers having entered clinical practice. AREAS COVERED This article covers extensive recent research that has established novel potential biomarkers based on genomics, proteomics, and clinical characteristics. Validating and incorporating these biomarkers into clinical practice can improve prognosis, prediction of recurrence, and treatment response. Relevant literature was collected from PubMed, Scopus, and clinicaltrials.gov databases (November 2023). EXPERT OPINION Currently, defining prognostic markers in soft tissue sarcomas remains challenging. More studies are required, especially to personalize treatment through advanced genetic profiling and analysis using individual tumor and patient characteristics.
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Affiliation(s)
- Anna M Czarnecka
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- Department of Experimental Pharmacology, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Paulina Chmiel
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- Medical Faculty, Warsaw Medical University, Warsaw, Poland
| | - Piotr Błoński
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- Medical Faculty, Warsaw Medical University, Warsaw, Poland
| | - Piotr Rutkowski
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
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Moura DS, Mondaza-Hernandez JL, Sanchez-Bustos P, Peña-Chilet M, Cordero-Varela JA, Lopez-Alvarez M, Carrillo-Garcia J, Martin-Ruiz M, Romero-Gonzalez P, Renshaw-Calderon M, Ramos R, Marcilla D, Alvarez-Alegret R, Agra-Pujol C, Izquierdo F, Ortega-Medina L, Martin-Davila F, Hernandez-Leon CN, Romagosa C, Salgado MAV, Lavernia J, Bagué S, Mayodormo-Aranda E, Alvarez R, Valverde C, Martinez-Trufero J, Castilla-Ramirez C, Gutierrez A, Dopazo J, Hindi N, Garcia-Foncillas J, Martin-Broto J. HMGA1 regulates trabectedin sensitivity in advanced soft-tissue sarcoma (STS): A Spanish Group for Research on Sarcomas (GEIS) study. Cell Mol Life Sci 2024; 81:219. [PMID: 38758230 PMCID: PMC11101398 DOI: 10.1007/s00018-024-05250-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 04/10/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024]
Abstract
HMGA1 is a structural epigenetic chromatin factor that has been associated with tumor progression and drug resistance. Here, we reported the prognostic/predictive value of HMGA1 for trabectedin in advanced soft-tissue sarcoma (STS) and the effect of inhibiting HMGA1 or the mTOR downstream pathway in trabectedin activity. The prognostic/predictive value of HMGA1 expression was assessed in a cohort of 301 STS patients at mRNA (n = 133) and protein level (n = 272), by HTG EdgeSeq transcriptomics and immunohistochemistry, respectively. The effect of HMGA1 silencing on trabectedin activity and gene expression profiling was measured in leiomyosarcoma cells. The effect of combining mTOR inhibitors with trabectedin was assessed on cell viability in vitro studies, whereas in vivo studies tested the activity of this combination. HMGA1 mRNA and protein expression were significantly associated with worse progression-free survival of trabectedin and worse overall survival in STS. HMGA1 silencing sensitized leiomyosarcoma cells for trabectedin treatment, reducing the spheroid area and increasing cell death. The downregulation of HGMA1 significantly decreased the enrichment of some specific gene sets, including the PI3K/AKT/mTOR pathway. The inhibition of mTOR, sensitized leiomyosarcoma cultures for trabectedin treatment, increasing cell death. In in vivo studies, the combination of rapamycin with trabectedin downregulated HMGA1 expression and stabilized tumor growth of 3-methylcholantrene-induced sarcoma-like models. HMGA1 is an adverse prognostic factor for trabectedin treatment in advanced STS. HMGA1 silencing increases trabectedin efficacy, in part by modulating the mTOR signaling pathway. Trabectedin plus mTOR inhibitors are active in preclinical models of sarcoma, downregulating HMGA1 expression levels and stabilizing tumor growth.
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Affiliation(s)
- David S Moura
- Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28015, Madrid, Spain.
- Department of Oncology in University Hospital Fundación Jiménez Díaz,, Av. de los Reyes Católicos, 2, 28040, Madrid, Spain.
| | - Jose L Mondaza-Hernandez
- Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28015, Madrid, Spain
| | - Paloma Sanchez-Bustos
- Institute of Biomedicine of Seville (IBIS, HUVR, CSIC, Universidad de Sevilla), 41013, Seville, Spain
| | - Maria Peña-Chilet
- Institute of Biomedicine of Seville (IBIS, HUVR, CSIC, Universidad de Sevilla), 41013, Seville, Spain
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, 41013, Seville, Spain
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, 41013, Seville, Spain
| | - Juan A Cordero-Varela
- Institute of Biomedicine of Seville (IBIS, HUVR, CSIC, Universidad de Sevilla), 41013, Seville, Spain
| | - Maria Lopez-Alvarez
- Institute of Biomedicine of Seville (IBIS, HUVR, CSIC, Universidad de Sevilla), 41013, Seville, Spain
| | - Jaime Carrillo-Garcia
- Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28015, Madrid, Spain
| | - Marta Martin-Ruiz
- Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28015, Madrid, Spain
| | - Pablo Romero-Gonzalez
- Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28015, Madrid, Spain
| | - Marta Renshaw-Calderon
- Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28015, Madrid, Spain
| | - Rafael Ramos
- Pathology Department, Son Espases University Hospital, 07120, Mallorca, Spain
| | - David Marcilla
- Pathology Department, University Hospital Virgen del Rocio, 41013, Seville, Spain
| | | | - Carolina Agra-Pujol
- Pathology Department, Gregorio Marañon Universitary Hospital, 28007, Madrid, Spain
| | - Francisco Izquierdo
- Pathological Anatomy Service, Complejo Asistencial Universitario de León, 24071, Leon, Spain
| | | | | | | | - Cleofe Romagosa
- Pathology department, Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | | | - Javier Lavernia
- Medical Oncology Department, Instituto Valenciano de Oncologia, 46009, Valencia, Spain
| | - Silvia Bagué
- Pathology Department, Hospital de la Santa Creu i Sant Pau, 08025, Barcelona, Spain
| | | | - Rosa Alvarez
- Medical Oncology Department, Gregorio Marañon Universitary Hospital, 28007, Madrid, Spain
| | - Claudia Valverde
- Medical Oncology Department, Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | | | | | - Antonio Gutierrez
- Hematology Department, Son Espases University Hospital, 07120, Mallorca, Spain
| | - Joaquin Dopazo
- Institute of Biomedicine of Seville (IBIS, HUVR, CSIC, Universidad de Sevilla), 41013, Seville, Spain
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, 41013, Seville, Spain
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, 41013, Seville, Spain
- INB-ELIXIR-es, FPS, Hospital Virgen del Rocío, 41013, Seville, Spain
| | - Nadia Hindi
- Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28015, Madrid, Spain
- Medical Oncology Department, Fundación Jimenez Diaz University Hospital, 28040, Madrid, Spain
- General de Villalba University Hospital, 28400, Madrid, Spain
| | - Jesus Garcia-Foncillas
- Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28015, Madrid, Spain
- Medical Oncology Department, Fundación Jimenez Diaz University Hospital, 28040, Madrid, Spain
- General de Villalba University Hospital, 28400, Madrid, Spain
| | - Javier Martin-Broto
- Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28015, Madrid, Spain.
- Medical Oncology Department, Fundación Jimenez Diaz University Hospital, 28040, Madrid, Spain.
- General de Villalba University Hospital, 28400, Madrid, Spain.
- Department of Oncology in University Hospital Fundación Jiménez Díaz,, Av. de los Reyes Católicos, 2, 28040, Madrid, Spain.
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8
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Fattori A, Reita D, Brinkert D, Willaume T, Gantzer J, Karanian M, Lhermitte B, Wolf T, De Pinieux G, Weingertner N. Coxal giant cell-rich tumour harbouring an NUTM1 gene fusion: a new molecular subtype of giant cell tumour of bone? Histopathology 2024; 84:1072-1075. [PMID: 38229224 DOI: 10.1111/his.15139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/19/2023] [Accepted: 12/30/2023] [Indexed: 01/18/2024]
Affiliation(s)
- Antonin Fattori
- Department of Pathology, Strasbourg University Hospital, Strasbourg, France
| | - Damien Reita
- Department of Cancer Molecular Genetics, Laboratory of Biochemistry and Molecular Biology, Strasbourg University Hospital, Strasbourg, France
| | - David Brinkert
- Department of Orthopedic Surgery and Traumatology, Strasbourg University Hospital, Strasbourg, France
| | - Thibault Willaume
- Department of Radiology, Strasbourg University Hospital, Strasbourg, France
| | - Justine Gantzer
- Department of Medical Oncology, Strasbourg-Europe Cancer Institute, Strasbourg, France
| | - Marie Karanian
- Department of Biopathology, Centre Léon Bérard, Lyon, France
| | - Benoit Lhermitte
- Department of Pathology, Strasbourg University Hospital, Strasbourg, France
| | - Thibaut Wolf
- Department of Pathology, Strasbourg University Hospital, Strasbourg, France
| | | | - Noëlle Weingertner
- Department of Pathology, Strasbourg University Hospital, Strasbourg, France
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9
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Subramanian A, Nemat-Gorgani N, Ellis-Caleo TJ, van IJzendoorn DGP, Sears TJ, Somani A, Luca BA, Zhou MY, Bradic M, Torres IA, Oladipo E, New C, Kenney DE, Avedian RS, Steffner RJ, Binkley MS, Mohler DG, Tap WD, D'Angelo SP, van de Rijn M, Ganjoo KN, Bui NQ, Charville GW, Newman AM, Moding EJ. Sarcoma microenvironment cell states and ecosystems are associated with prognosis and predict response to immunotherapy. NATURE CANCER 2024; 5:642-658. [PMID: 38429415 PMCID: PMC11058033 DOI: 10.1038/s43018-024-00743-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 02/08/2024] [Indexed: 03/03/2024]
Abstract
Characterization of the diverse malignant and stromal cell states that make up soft tissue sarcomas and their correlation with patient outcomes has proven difficult using fixed clinical specimens. Here, we employed EcoTyper, a machine-learning framework, to identify the fundamental cell states and cellular ecosystems that make up sarcomas on a large scale using bulk transcriptomes with clinical annotations. We identified and validated 23 sarcoma-specific, transcriptionally defined cell states, many of which were highly prognostic of patient outcomes across independent datasets. We discovered three conserved cellular communities or ecotypes associated with underlying genomic alterations and distinct clinical outcomes. We show that one ecotype defined by tumor-associated macrophages and epithelial-like malignant cells predicts response to immune-checkpoint inhibition but not chemotherapy and validate our findings in an independent cohort. Our results may enable identification of patients with soft tissue sarcomas who could benefit from immunotherapy and help develop new therapeutic strategies.
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Affiliation(s)
- Ajay Subramanian
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Neda Nemat-Gorgani
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | | | | | - Timothy J Sears
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Anish Somani
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Bogdan A Luca
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Maggie Y Zhou
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Martina Bradic
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ileana A Torres
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Eniola Oladipo
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Christin New
- Department of Orthopedic Surgery, Stanford University, Stanford, CA, USA
| | - Deborah E Kenney
- Department of Orthopedic Surgery, Stanford University, Stanford, CA, USA
| | - Raffi S Avedian
- Department of Orthopedic Surgery, Stanford University, Stanford, CA, USA
| | - Robert J Steffner
- Department of Orthopedic Surgery, Stanford University, Stanford, CA, USA
| | - Michael S Binkley
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - David G Mohler
- Department of Orthopedic Surgery, Stanford University, Stanford, CA, USA
| | - William D Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical Center, New York, NY, USA
| | - Sandra P D'Angelo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical Center, New York, NY, USA
| | | | - Kristen N Ganjoo
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Nam Q Bui
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | | | - Aaron M Newman
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Everett J Moding
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
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10
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Park C, Kim R, Choi J, Kim M, Kim TM, Han I, Kim JI, Kim HS. Case Series of Soft Tissue Sarcoma Patients with Brain Metastasis with Implications from Genomic and Transcriptomic Analysis. Cancer Res Treat 2024; 56:665-674. [PMID: 37752792 PMCID: PMC11016652 DOI: 10.4143/crt.2023.864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/26/2023] [Indexed: 09/28/2023] Open
Abstract
PURPOSE Brain metastasis rarely occurs in soft tissue sarcoma (STS). Here, we present five cases of STS with brain metastases with genetic profiles. MATERIALS AND METHODS We included five patients from Seoul National University Hospital who were diagnosed with STS with metastasis to the brain. Tissue from the brain metastasis along with that from the primary site or other metastases were used for DNA and RNA sequencing to identify genetic profiles. Gene expression profiles were compared with sarcoma samples from The Cancer Genome Atlas. RESULTS The overall survival after diagnosis of brain metastasis ranged from 2.2 to 34.3 months. Comparison of mutational profiles between brain metastases and matched primary or other metastatic samples showed similar profiles. In two patients, copy number variation profiles between brain metastasis and other tumors showed several differences including MYCL, JUN, MYC, and DDR2 amplification. Gene ontology analysis showed that the group of genes significantly highly expressed in the brain metastasis samples was enriched in the G-protein coupled receptor activity, structural constituent of chromatin, protein heterodimerization activity, and binding of DNA, RNA, and protein. Gene set enrichment analysis showed enrichment in the pathway of neuroactive ligand-receptor interaction and systemic lupus erythematosus. CONCLUSION The five patients had variable ranges of clinical courses and outcomes. Genomic and transcriptomic analysis of STS with brain metastasis implicates possible involvement of complex expression modification and epigenetic changes rather than the addition of single driver gene alteration.
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Affiliation(s)
- Changhee Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Rokhyun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea
| | - Jaeyong Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea
| | - Miso Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Tae Min Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Ilkyu Han
- Department of Orthopaedic Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Han-Soo Kim
- Department of Orthopaedic Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
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11
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Ewongwo A, Hui C, Moding EJ. Opportunity in Complexity: Harnessing Molecular Biomarkers and Liquid Biopsies for Personalized Sarcoma Care. Semin Radiat Oncol 2024; 34:195-206. [PMID: 38508784 DOI: 10.1016/j.semradonc.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Due to their rarity and complexity, sarcomas represent a substantial therapeutic challenge. However, the incredible diversity within and across sarcoma subtypes presents an opportunity for personalized care to maximize efficacy and limit toxicity. A deeper understanding of the molecular alterations that drive sarcoma development and treatment response has paved the way for molecular biomarkers to shape sarcoma treatment. Genetic, transcriptomic, and protein biomarkers have become critical tools for diagnosis, prognostication, and treatment selection in patients with sarcomas. In the future, emerging biomarkers like circulating tumor DNA analysis offer the potential to improve early detection, monitoring response to treatment, and identifying mechanisms of resistance to personalize sarcoma treatment. Here, we review the current state of molecular biomarkers for sarcomas and highlight opportunities and challenges for the implementation of new technologies in the future.
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Affiliation(s)
- Agnes Ewongwo
- Department of Radiation Oncology, Stanford University, Stanford, CA
| | - Caressa Hui
- Department of Radiation Oncology, Stanford University, Stanford, CA
| | - Everett J Moding
- Department of Radiation Oncology, Stanford University, Stanford, CA.; Stanford Cancer Institute, Stanford University, Stanford, CA..
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12
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Patton A, Dermawan JK. Current updates in sarcoma biomarker discovery: emphasis on next-generation sequencing-based methods. Pathology 2024; 56:274-282. [PMID: 38185613 DOI: 10.1016/j.pathol.2023.10.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/25/2023] [Accepted: 10/29/2023] [Indexed: 01/09/2024]
Abstract
Soft tissue sarcomas comprise a heterogeneous group of neoplasms. Although soft tissue malignancies make up only 2% of adult cancers, classification based on histomorphology presents a diagnostic challenge. Characterisation of soft tissue sarcomas by molecular analysis is rapidly evolving to improve diagnostic accuracy and develop targeted therapies. This review highlights the advances in molecular techniques, including current next-generation sequencing-based assays (fusion detection by RNA sequencing, targeted/whole exome sequencing, microRNA profiling), as well as emerging methods (liquid biopsies, DNA methylation profiling, single-cell molecular profiling and next-generation immunohistochemistry) for future clinical applications.
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Affiliation(s)
- Ashley Patton
- Department of Pathology & Laboratory Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Josephine K Dermawan
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA.
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13
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Beaudier P, Vilotte F, Simon M, Muggiolu G, Le Trequesser Q, Devès G, Plawinski L, Mikael A, Caron J, Kantor G, Dupuy D, Delville MH, Barberet P, Seznec H. Sarcoma cell-specific radiation sensitization by titanate scrolled nanosheets: insights from physicochemical analysis and transcriptomic profiling. Sci Rep 2024; 14:3295. [PMID: 38332121 PMCID: PMC10853196 DOI: 10.1038/s41598-024-53847-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/06/2024] [Indexed: 02/10/2024] Open
Abstract
This study aimed to explore the potential of metal oxides such as Titanate Scrolled Nanosheets (TNs) in improving the radiosensitivity of sarcoma cell lines. Enhancing the response of cancer cells to radiation therapy is crucial, and one promising approach involves utilizing metal oxide nanoparticles. We focused on the impact of exposing two human sarcoma cell lines to both TNs and ionizing radiation (IR). Our research was prompted by previous in vitro toxicity assessments, revealing a correlation between TNs' toxicity and alterations in intracellular calcium homeostasis. A hydrothermal process using titanium dioxide powder in an alkaline solution produced the TNs. Our study quantified the intracellular content of TNs and analyzed their impact on radiation-induced responses. This assessment encompassed PIXE analysis, cell proliferation, and transcriptomic analysis. We observed that sarcoma cells internalized TNs, causing alterations in intracellular calcium homeostasis. We also found that irradiation influence intracellular calcium levels. Transcriptomic analysis revealed marked disparities in the gene expression patterns between the two sarcoma cell lines, suggesting a potential cell-line-dependent nano-sensitization to IR. These results significantly advance our comprehension of the interplay between TNs, IR, and cancer cells, promising potential enhancement of radiation therapy efficiency.
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Affiliation(s)
- Pierre Beaudier
- UMR 5797, LP2I Bordeaux, CNRS, University of Bordeaux, 33170, Gradignan, France
- U1212, IECB, INSERM, University of Bordeaux, 33607, Pessac, France
| | - Florent Vilotte
- UMR 5797, LP2I Bordeaux, CNRS, University of Bordeaux, 33170, Gradignan, France
- Radiation Oncology Unit, Institut Bergonié, 33076, Bordeaux, France
| | - Marina Simon
- UMR 5797, LP2I Bordeaux, CNRS, University of Bordeaux, 33170, Gradignan, France
| | - Giovanna Muggiolu
- UMR 5797, LP2I Bordeaux, CNRS, University of Bordeaux, 33170, Gradignan, France
| | | | - Guillaume Devès
- UMR 5797, LP2I Bordeaux, CNRS, University of Bordeaux, 33170, Gradignan, France
| | - Laurent Plawinski
- UMR 5797, LP2I Bordeaux, CNRS, University of Bordeaux, 33170, Gradignan, France
| | - Antoine Mikael
- Radiation Oncology Unit, Institut Bergonié, 33076, Bordeaux, France
| | - Jérôme Caron
- Radiation Oncology Unit, Institut Bergonié, 33076, Bordeaux, France
| | - Guy Kantor
- Radiation Oncology Unit, Institut Bergonié, 33076, Bordeaux, France
| | - Denis Dupuy
- U1212, IECB, INSERM, University of Bordeaux, 33607, Pessac, France
| | | | - Philippe Barberet
- UMR 5797, LP2I Bordeaux, CNRS, University of Bordeaux, 33170, Gradignan, France
| | - Hervé Seznec
- UMR 5797, LP2I Bordeaux, CNRS, University of Bordeaux, 33170, Gradignan, France.
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14
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Laroche-Clary A, Josensi C, Derieppe MA, Belhomme S, Vendrely V, Perret R, Cadogan E, Italiano A. Selective DNA-PK Inhibition Enhances Chemotherapy and Ionizing Radiation Activity in Soft-Tissue Sarcomas. Clin Cancer Res 2024; 30:629-637. [PMID: 37982819 DOI: 10.1158/1078-0432.ccr-23-1531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/25/2023] [Accepted: 11/16/2023] [Indexed: 11/21/2023]
Abstract
PURPOSE Patients with advanced soft-tissue sarcomas (STS) exhibit a poor prognosis and have few therapeutic options. DNA-dependent protein kinase (DNA-PK) catalytic subunit is a multifunctional serine-threonine protein kinase that plays a crucial role in DNA double-strand damage repair via nonhomologous end joining. EXPERIMENTAL DESIGN To investigate the therapeutic potential of DNA-PK targeting in STS, we first evaluated the prognostic value of DNA-PK expression in two large cohorts of patients with STS. We then used the potent and selective DNA-PK inhibitor AZD7648 compound to investigate the antitumor effect of the pharmacologic inhibition of DNA-PK in vitro via MTT, apoptosis, cell cycle, and proliferation assays. In vivo studies were performed with patient-derived xenograft models to evaluate the effects of AZD7648 in combination with chemotherapy or ionizing radiation on tumor growth. The mechanisms of sensitivity and resistance to DNA-PK inhibition were investigated by using a genome-wide CRISPR-Cas9 positive screen. RESULTS DNA-PK overexpression is significantly associated with poor prognosis in patients with sarcomas. Selective pharmacologic inhibition of DNA-PK strongly synergizes with radiation- and doxorubicin-based regimen in sarcoma models. By using a genome-wide CRISPR-Cas9 positive screen, we identified genes involved in sensitivity to DNA-PK inhibition. CONCLUSIONS DNA-PK inhibition deserves clinical investigation to improve response to current therapies in patients with sarcoma.
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Affiliation(s)
- Audrey Laroche-Clary
- Sarcoma Unit, Institut Bergonié, Bordeaux, France
- INSERM, U1312, Bordeaux, France
| | - Coralie Josensi
- Sarcoma Unit, Institut Bergonié, Bordeaux, France
- INSERM, U1312, Bordeaux, France
| | | | - Sarah Belhomme
- Department of Radiation Therapy, Institut Bergonié, Bordeaux, France
| | | | - Raul Perret
- Department of Pathology, Institut Bergonié, Bordeaux, France
| | | | - Antoine Italiano
- Sarcoma Unit, Institut Bergonié, Bordeaux, France
- INSERM, U1312, Bordeaux, France
- Faculty of Medicine, University of Bordeaux, Bordeaux, France
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15
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Llacer-Moscardo C, Moureau-Zabotto L, Ollivier L, Helfré S, Ducassou A, Bonvalot S, Sunyach MP, Sargos P, Gillon P, Firmin N, Le Péchoux C, Thariat J. Management of oligometastatic/metastatic sarcomas and place of local treatments with focus on modern radiotherapy approaches. Cancer Radiother 2024; 28:93-102. [PMID: 38212215 DOI: 10.1016/j.canrad.2023.06.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/09/2023] [Accepted: 06/29/2023] [Indexed: 01/13/2024]
Abstract
Soft tissue sarcomas are a rare and heterogeneous disease. For localized disease, treatment is based on surgery and radiotherapy with or without chemotherapy depending on risk factors. Upfront metastases are present in 7 to 20% of cases, and are localized to the lungs in most of cases. Disseminated disease is generally considered incurable but in selected cases, aggressive local treatment of metastases allowed long survival. Treatment of primary tumour is often debated. Our purpose is to evaluate the literature concerning the role of radiotherapy in the management of primary metastatic soft tissue sarcomas.
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Affiliation(s)
- C Llacer-Moscardo
- Radiation oncology department, institut du cancer de Montpellier (ICM), 208, avenue des Apothicaires, parc Euromédecine, 34298 Montpellier cedex 5, France.
| | - L Moureau-Zabotto
- Department of radiotherapy, centre de radiothérapie du Pays d'Aix, avenue Henri-Pontier, 13100 Aix-en-Provence, France
| | - L Ollivier
- Department of radiotherapy, institut de cancérologie de l'Ouest (ICO), centre René-Gauducheau, Saint-Herblain, France
| | - S Helfré
- Department of radiotherapy, institut Curie, 26, rue d'Ulm, 75005 Paris, France
| | - A Ducassou
- Department of radiotherapy, IUCT Oncopole, 1, avenue Irène-Joliot-Curie, 31100 Toulouse, France
| | - S Bonvalot
- Department of oncological surgery, institut Curie, 26, rue d'Ulm, 75005 Paris, France
| | - M-P Sunyach
- Department of radiotherapy, centre Léon-Bérard, 28, promenade Léa-et-Napoléon-Bullukian, 69008 Lyon, France
| | - P Sargos
- Department of radiotherapy, institut Bergonié, 229, cours de l'Argonne, 33076 Bordeaux, France
| | - P Gillon
- Department of radiotherapy, institut Bergonié, 229, cours de l'Argonne, 33076 Bordeaux, France
| | - N Firmin
- Radiation oncology department, institut du cancer de Montpellier (ICM), 208, avenue des Apothicaires, parc Euromédecine, 34298 Montpellier cedex 5, France
| | - C Le Péchoux
- Department of radiotherapy, Gustave-Roussy, 114, rue Édouard-Vaillant, 94805 Villejuif, France
| | - J Thariat
- Department of radiotherapy, centre François-Baclesse, 12, rue Jean-Baptiste-Colbert, 14000 Caen, France
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16
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Crombé A, Bertolo F, Vanhersecke L, Guegan JP, Bessede A, Perret R, Le Loarer F, Chaire V, Coindre JM, Lucchesi C, Italiano A. Deciphering the correlation between metabolic activity through 18F-FDG-PET/CT and immune landscape in soft-tissue sarcomas: an insight from the NEOSARCOMICS study. Biomark Res 2024; 12:3. [PMID: 38185642 PMCID: PMC10773028 DOI: 10.1186/s40364-023-00552-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/19/2023] [Indexed: 01/09/2024] Open
Abstract
Metabolic elevation in soft-tissue sarcomas (STS), as documented with 18F-Fluorodeoxyglucose positron emission tomography (18F-FDG-PET/CT) has been linked with cell proliferation, higher grade, and lower survivals. However, the recent diagnostic innovations (CINSARC gene-expression signature and tertiary lymphoid structure [TLS]) and therapeutic innovations (immune checkpoint inhibitors [ICIs]) for STS patients underscore the need to re-assess the role of 18F-FDG-PET/CT. Thus, in this correspondence, our objective was to investigate the correlations between STS metabolism as assessed by nuclear imaging, and the immune landscape as estimated by transcriptomics analysis, immunohistochemistry panels, and TLS assessment. Based on a prospective cohort of 85 adult patients with high-grade STS recruited in the NEOSARCOMICS trial (NCT02789384), we identified 3 metabolic groups according to 18F-FDG-PET/CT metrics (metabolic-low [60%], -intermediate [15.3%] and high [24.7%]). We found that T-cells CD8 pathway was significantly enriched in metabolic-high STS. Conversely, several pathways involved in antitumor immune response, cell differentiation and cell cycle, were downregulated in extreme metabolic-low STS. Next, multiplex immunofluorescence showed that densities of CD8+, CD14+, CD45+, CD68+, and c-MAF cells were significantly higher in the metabolic-high group compared to the metabolic-low group. Lastly, no association was found between metabolic group and TLS status. Overall, these results suggest that (i) rapidly proliferating and metabolically active STS can instigate a more robust immune response, thereby attracting immune cells such as T cells and macrophages, and (ii) metabolic activity and TLS could independently influence immune responses.
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Affiliation(s)
- Amandine Crombé
- Department of Oncologic Imaging, Comprehensive Cancer Center, Institut Bergonié, Bordeaux, F-33076, France.
- Department of Musculoskeletal Imaging, Pellegrin University Hospital, Bordeaux, F-33000, France.
- SARCOTARGET Team, Bordeaux Institute of Oncology (BRIC) INSERM U1312, Bordeaux, F-33076, France.
| | - Frédéric Bertolo
- Department of Bioinformatics, Comprehensive Cancer Center, Institut Bergonié, Bordeaux, F-33076, France
| | - Lucile Vanhersecke
- Department of Pathology, Comprehensive Cancer Center, Institut Bergonié, Bordeaux, F-33076, France
| | | | | | - Raul Perret
- Department of Pathology, Comprehensive Cancer Center, Institut Bergonié, Bordeaux, F-33076, France
| | - François Le Loarer
- SARCOTARGET Team, Bordeaux Institute of Oncology (BRIC) INSERM U1312, Bordeaux, F-33076, France
- Department of Pathology, Comprehensive Cancer Center, Institut Bergonié, Bordeaux, F-33076, France
| | - Vanessa Chaire
- SARCOTARGET Team, Bordeaux Institute of Oncology (BRIC) INSERM U1312, Bordeaux, F-33076, France
- Department of Pathology, Comprehensive Cancer Center, Institut Bergonié, Bordeaux, F-33076, France
| | - Jean-Michel Coindre
- SARCOTARGET Team, Bordeaux Institute of Oncology (BRIC) INSERM U1312, Bordeaux, F-33076, France
- Department of Pathology, Comprehensive Cancer Center, Institut Bergonié, Bordeaux, F-33076, France
| | - Carlo Lucchesi
- Department of Bioinformatics, Comprehensive Cancer Center, Institut Bergonié, Bordeaux, F-33076, France
| | - Antoine Italiano
- SARCOTARGET Team, Bordeaux Institute of Oncology (BRIC) INSERM U1312, Bordeaux, F-33076, France
- Department of Medical Oncology, Comprehensive Cancer Center, Institut Bergonié, Bordeaux, F-33076, France
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17
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Nardi W, Nicolas N, El Zein S, Tzanis D, Bouhadiba T, Helfre S, Watson S, Brisse HJ, Servois V, Bonvalot S. Diagnostic accuracy and safety of percutaneous core needle biopsy of retroperitoneal tumours. EUROPEAN JOURNAL OF SURGICAL ONCOLOGY 2024; 50:107298. [PMID: 38086314 DOI: 10.1016/j.ejso.2023.107298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/10/2023] [Accepted: 11/21/2023] [Indexed: 01/16/2024]
Abstract
BACKGROUND Histologic subtype of cancer guides treatment sequencing and the extent of surgery for retroperitoneal tumours (RPTs) but concerns persist regarding percutaneous core needle biopsy (CNB). OBJECTIVE Endpoints were the incidence of early complications, needle tract seeding (NTS) after CNB, diagnostic accuracy. METHODS Between 2015 and 2022, data from patients with RPT who underwent a CNB and who operated on at Institut Curie were collected. We retrospectively reviewed the medical records and microscopic analysis of both CNB and surgical specimens to evaluate the diagnostic accuracy of CNB (quantified using positive and negative predictive values, PPV/NPV). RESULTS 313 patients underwent CNB. In 10/326 (3 %) procedures, minor complications were observed. One of 212 (0.47 %) resected RPSs exhibited a local recurrence compatible with NTS. Microscopic analysis of CNB specimens allowed the classification of tumours between groups of cancers and benign/intermediate mesenchymal tumours in 307/313 (98 %) patients. Among the 204 patients with retroperitoneal sarcoma, the overall concordance between CNB and final pathology following resection was 178/204 (87.2 %). The respective PPVs of solitary fibrous tumour, dedifferentiated liposarcoma, leiomyosarcoma and well-differentiated liposarcoma were 100 %, 98 %, 97 % and 68 %, respectively. The diagnosis of a high-grade (G 2-3) sarcoma resulted in a high specificity (97 %) and PPV (98 %) but low sensitivity (76 %). CONCLUSIONS CNB allowed the classification of RPT in the vast majority of patients with a low morbidity rate. Concordance with final diagnosis was high for sarcomas with the exception of well-differentiated liposarcoma. As a result, CNB results should be integrated with imaging/radiomics by multidisciplinary tumour boards.
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Affiliation(s)
- Walter Nardi
- Department of Surgical Oncology, Institut Curie, Paris, France; Department of General Surgery, Surgical Oncology Unit, Buenos Aires British Hospital, Buenos Aires, Argentina.
| | | | - Sophie El Zein
- Department of Biopathology, Institut Curie, Paris, France.
| | - Dimitri Tzanis
- Department of Surgical Oncology, Institut Curie, Paris, France.
| | | | - Sylvie Helfre
- Department of Radiotherapy, Institut Curie, Paris, France.
| | - Sarah Watson
- Department of Medical Oncology and INSERM U830, Institut Curie, Paris, France.
| | | | | | - Sylvie Bonvalot
- Department of Surgical Oncology, Institut Curie, Paris, France.
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18
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Crombé A, Spinnato P, Italiano A, Brisse HJ, Feydy A, Fadli D, Kind M. Radiomics and artificial intelligence for soft-tissue sarcomas: Current status and perspectives. Diagn Interv Imaging 2023; 104:567-583. [PMID: 37802753 DOI: 10.1016/j.diii.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 10/08/2023]
Abstract
This article proposes a summary of the current status of the research regarding the use of radiomics and artificial intelligence to improve the radiological assessment of patients with soft tissue sarcomas (STS), a heterogeneous group of rare and ubiquitous mesenchymal malignancies. After a first part explaining the principle of radiomics approaches, from raw image post-processing to extraction of radiomics features mined with unsupervised and supervised machine-learning algorithms, and the current research involving deep learning algorithms in STS, especially convolutional neural networks, this review details their main research developments since the formalisation of 'radiomics' in oncologic imaging in 2010. This review focuses on CT and MRI and does not involve ultrasonography. Radiomics and deep radiomics have been successfully applied to develop predictive models to discriminate between benign soft-tissue tumors and STS, to predict the histologic grade (i.e., the most important prognostic marker of STS), the response to neoadjuvant chemotherapy and/or radiotherapy, and the patients' survivals and probability for presenting distant metastases. The main findings, limitations and expectations are discussed for each of these outcomes. Overall, after a first decade of publications emphasizing the potential of radiomics through retrospective proof-of-concept studies, almost all positive but with heterogeneous and often non-replicable methods, radiomics is now at a turning point in order to provide robust demonstrations of its clinical impact through open-science, independent databases, and application of good and standardized practices in radiomics such as those provided by the Image Biomarker Standardization Initiative, without forgetting innovative research paths involving other '-omics' data to better understand the relationships between imaging of STS, gene-expression profiles and tumor microenvironment.
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Affiliation(s)
- Amandine Crombé
- Department of Radiology, Pellegrin University Hospital, 33000 Bordeaux, France; Department of Oncologic Imaging, Bergonié Institute, 33076 Bordeaux, France; 'Sarcotarget' team, BRIC INSERM U1312 and Bordeaux University, 33000 Bordeaux France.
| | - Paolo Spinnato
- Diagnostic and Interventional Radiology, IRCCS Istituto Ortopedico Rizzoli, Bologna 40136, Italy
| | | | | | - Antoine Feydy
- Department of Radiology, Hopital Cochin-AP-HP, 75014 Paris, France; Université Paris Cité, Faculté de Médecine, 75006 Paris, France
| | - David Fadli
- Department of Radiology, Pellegrin University Hospital, 33000 Bordeaux, France
| | - Michèle Kind
- Department of Oncologic Imaging, Bergonié Institute, 33076 Bordeaux, France
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19
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Wallander K, Öfverholm I, Boye K, Tsagkozis P, Papakonstantinou A, Lin Y, Haglund de Flon F. Sarcoma care in the era of precision medicine. J Intern Med 2023; 294:690-707. [PMID: 37643281 DOI: 10.1111/joim.13717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Sarcoma subtype classification is currently mainly based upon histopathological morphology. Molecular analyses have emerged as an efficient addition to the diagnostic workup and sarcoma care. Knowledge about the sarcoma genome increases, and genetic events that can either support a histopathological diagnosis or suggest a differential diagnosis are identified, as well as novel therapeutic targets. In this review, we present diagnostic, therapeutic, and prognostic molecular markers that are, or might soon be, used clinically. For sarcoma diagnostics, there are specific fusions highly supportive or pathognomonic for a diagnostic entity-for instance, SYT::SSX in synovial sarcoma. Complex karyotypes also give diagnostic information-for example, supporting dedifferentiation rather than low-grade central osteosarcoma or well-differentiated liposarcoma when detected in combination with MDM2/CDK4 amplification. Molecular treatment predictive sarcoma markers are available for gastrointestinal stromal tumor (GIST) and locally aggressive benign mesenchymal tumors. The molecular prognostic markers for sarcomas in clinical practice are few. For solitary fibrous tumor, the type of NAB2::STAT6 fusion is associated with the outcome, and the KIT/PDGFRA pathogenic variant in GISTs can give prognostic information. With the exploding availability of sequencing technologies, it becomes increasingly important to understand the strengths and limitations of those methods and their context in sarcoma diagnostics. It is reasonable to believe that most sarcoma treatment centers will increase the use of massive-parallel sequencing soon. We conclude that the context in which the genetic findings are interpreted is of importance, and the interpretation of genomic findings requires considering tumor histomorphology.
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Affiliation(s)
- Karin Wallander
- Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | | | - Kjetil Boye
- Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Panagiotis Tsagkozis
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Andri Papakonstantinou
- Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Breast Cancer, Endocrine Tumors and Sarcoma, Karolinska University Hospital and Karolinska Comprehensive Cancer Centre, Stockholm, Sweden
| | - Yingbo Lin
- Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Felix Haglund de Flon
- Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Pathology and Cancer diagnostics, Karolinska University Hospital, Stockholm, Sweden
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20
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Kokkali S, Georgaki E, Mandrakis G, Valverde C, Theocharis S. Genomic Profiling and Clinical Outcomes of Targeted Therapies in Adult Patients with Soft Tissue Sarcomas. Cells 2023; 12:2632. [PMID: 37998367 PMCID: PMC10670373 DOI: 10.3390/cells12222632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
Genomic profiling has improved our understanding of the pathogenesis of different cancers and led to the development of several targeted therapies, especially in epithelial tumors. In this review, we focus on the clinical utility of next-generation sequencing (NGS) to inform therapeutics in soft tissue sarcoma (STS). The role of NGS is still controversial in patients with sarcoma, given the low mutational burden and the lack of recurrent targetable alterations in most of the sarcoma histotypes. The clinical impact of genomic profiling in STS has not been investigated prospectively. A limited number of retrospective, mainly single-institution, studies have addressed this issue using various NGS technologies and platforms and a variety of criteria to define a genomic alteration as actionable. Despite the detailed reports on the different gene mutations, fusions, or amplifications that were detected, data on the use and efficacy of targeted treatment are very scarce at present. With the exception of gastrointestinal stromal tumors (GISTs), these targeted therapies are administered either through off-label prescription of an approved drug or enrollment in a matched clinical trial. Based mainly on anecdotal reports, the outcome of targeted therapies in the different STS histotypes is discussed. Prospective studies are warranted to assess whether genomic profiling improves the management of STS patients.
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Affiliation(s)
- Stefania Kokkali
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece;
- Oncology Unit, 2nd Department of Medicine, Medical School, Hippocratio General Hospital of Athens, National and Kapodistrian University of Athens, V. Sofias 114, 11527 Athens, Greece;
| | - Eleni Georgaki
- Oncology Unit, 2nd Department of Medicine, Medical School, Hippocratio General Hospital of Athens, National and Kapodistrian University of Athens, V. Sofias 114, 11527 Athens, Greece;
| | - Georgios Mandrakis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece;
| | - Claudia Valverde
- Medical Oncology Department, Vall d’Hebron University Hospital, Pg. Vall d’Hebron 119-12, 08035 Barcelona, Spain;
| | - Stamatios Theocharis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece;
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21
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Tirotta F, Fadel MG, Baia M, Parente A, Messina V, Bassett P, Almond LM, Ford SJ, Desai A, van Houdt WJ, Strauss DC. Risk Factors for the Development of Early Recurrence in Patients with Primary Retroperitoneal Sarcoma. Ann Surg Oncol 2023; 30:6875-6883. [PMID: 37423926 DOI: 10.1245/s10434-023-13754-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/31/2023] [Indexed: 07/11/2023]
Abstract
BACKGROUND Disease recurrence after retroperitoneal sarcoma (RPS) surgery is common, and resection may offer no benefit for patients who experience recurrence early. This study examined the incidence of early recurrence (EREC) in RPS patients, and the association between EREC and prognosis, aiming to identify the factors associated with EREC. METHODS Patients undergoing surgery for primary RPS from 2008 to 2019 at two tertiary RPS centers were analyzed. The study defined EREC as any evidence of local recurrence and/or distant metastases on the CT scan up to 6 months after surgery. Overall survival (OS) was calculated using the Kaplan-Meier method. A multivariable analysis was performed to identify independent predictors of EREC. RESULTS Of the 692 patients who underwent surgery during the study period, 657 were included in the analysis. Sixty-five of these patients (9.9%; 95% confidence interval [CI], 7.7-12.4%) developed EREC. Five-year OS was 3% for the patients with EREC versus 76% for those without EREC (p < 0.001). Patient characteristics were compared between the EREC and non-EREC patients, and EREC was found to be significantly associated with Eastern Cooperative Oncology Group (ECOG) performance status (p = 0.006), tumor histology (p = 0.002), tumor grading (p < 0.001), radiotherapy (p = 0.04), and postoperative complications measured as a comprehensive complications index value (p = 0.003). However, the only significant independent predictor of EREC in the multivariable analysis was grade 3 tumors, with an odds ratio of 14.8 (95% CI, 4.44-49.2; p < 0.001). CONCLUSION Early recurrence is associated with a poor prognosis, and a high tumor grade is an independent predictor for the development of EREC. Patients with EREC may benefit the most from new therapeutic options such as neoadjuvant chemotherapy.
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Affiliation(s)
- Fabio Tirotta
- Department of Sarcoma and General Surgery, Midlands Abdominal and Retroperitoneal Sarcoma Unit, University Hospital Birmingham NHS Foundation Trust, Birmingham, UK.
| | - Michael G Fadel
- Department of Academic Surgery, Sarcoma Unit, The Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - Marco Baia
- Department of Sarcoma and General Surgery, Midlands Abdominal and Retroperitoneal Sarcoma Unit, University Hospital Birmingham NHS Foundation Trust, Birmingham, UK
- Sarcoma Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Alessandro Parente
- Department of Sarcoma and General Surgery, Midlands Abdominal and Retroperitoneal Sarcoma Unit, University Hospital Birmingham NHS Foundation Trust, Birmingham, UK
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Valentina Messina
- Department of Sarcoma and General Surgery, Midlands Abdominal and Retroperitoneal Sarcoma Unit, University Hospital Birmingham NHS Foundation Trust, Birmingham, UK
| | | | - L Max Almond
- Department of Sarcoma and General Surgery, Midlands Abdominal and Retroperitoneal Sarcoma Unit, University Hospital Birmingham NHS Foundation Trust, Birmingham, UK
| | - Samuel J Ford
- Department of Sarcoma and General Surgery, Midlands Abdominal and Retroperitoneal Sarcoma Unit, University Hospital Birmingham NHS Foundation Trust, Birmingham, UK
| | - Anant Desai
- Department of Sarcoma and General Surgery, Midlands Abdominal and Retroperitoneal Sarcoma Unit, University Hospital Birmingham NHS Foundation Trust, Birmingham, UK
| | - Winan J van Houdt
- Department of Surgical Oncology, The Netherlands Cancer Institute-Antoni van Leeuwenhoek, Plesmanlaan, Amsterdam, The Netherlands
| | - Dirk C Strauss
- Department of Academic Surgery, Sarcoma Unit, The Royal Marsden Hospital NHS Foundation Trust, London, UK
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22
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Sharaf R, Jin DX, Grady J, Napier C, Ebot E, Frampton GM, Albacker LA, Thomas DM, Montesion M. A pan-sarcoma landscape of telomeric content shows that alterations in RAD51B and GID4 are associated with higher telomeric content. NPJ Genom Med 2023; 8:26. [PMID: 37709802 PMCID: PMC10502097 DOI: 10.1038/s41525-023-00369-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/18/2023] [Indexed: 09/16/2023] Open
Abstract
Tumor cells need to activate a telomere maintenance mechanism, enabling limitless replication. The bulk of evidence supports that sarcomas predominantly use alternative lengthening of telomeres (ALT) mechanism, commonly associated with alterations in ATRX and DAXX. In our dataset, only 12.3% of sarcomas harbored alterations in these genes. Thus, we checked for the presence of other genomic determinants of high telomeric content in sarcomas. Our dataset consisted of 13555 sarcoma samples, sequenced as a part of routine clinical care on the FoundationOne®Heme platform. We observed a median telomeric content of 622.3 telomeric reads per GC-matched million reads (TRPM) across all samples. In agreement with previous studies, telomeric content was significantly higher in ATRX altered and POT1 altered sarcomas. We further observed that sarcomas with alterations in RAD51B or GID4 were enriched in samples with high telomeric content, specifically within uterus leiomyosarcoma for RAD51B and soft tissue sarcoma (not otherwise specified, nos) for GID4, Furthermore, RAD51B and POT1 alterations were mutually exclusive with ATRX and DAXX alterations, suggestive of functional redundancy. Our results propose a role played by RAD51B and GID4 in telomere elongation in sarcomas and open research opportunities for agents aimed at targeting this critical pathway in tumorigenesis.
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Affiliation(s)
| | | | - John Grady
- Omico Australian Genomic Cancer Medicine, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, Australia
| | - Christine Napier
- Omico Australian Genomic Cancer Medicine, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, Australia
| | - Ericka Ebot
- Foundation Medicine Inc., Cambridge, MA, USA
| | | | | | - David M Thomas
- Omico Australian Genomic Cancer Medicine, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, Australia
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23
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Belova T, Biondi N, Hsieh PH, Lutsik P, Chudasama P, Kuijjer M. Heterogeneity in the gene regulatory landscape of leiomyosarcoma. NAR Cancer 2023; 5:zcad037. [PMID: 37492373 PMCID: PMC10365024 DOI: 10.1093/narcan/zcad037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 07/06/2023] [Accepted: 07/18/2023] [Indexed: 07/27/2023] Open
Abstract
Characterizing inter-tumor heterogeneity is crucial for selecting suitable cancer therapy, as the presence of diverse molecular subgroups of patients can be associated with disease outcome or response to treatment. While cancer subtypes are often characterized by differences in gene expression, the mechanisms driving these differences are generally unknown. We set out to model the regulatory mechanisms driving sarcoma heterogeneity based on patient-specific, genome-wide gene regulatory networks. We developed a new computational framework, PORCUPINE, which combines knowledge on biological pathways with permutation-based network analysis to identify pathways that exhibit significant regulatory heterogeneity across a patient population. We applied PORCUPINE to patient-specific leiomyosarcoma networks modeled on data from The Cancer Genome Atlas and validated our results in an independent dataset from the German Cancer Research Center. PORCUPINE identified 37 heterogeneously regulated pathways, including pathways representing potential targets for treatment of subgroups of leiomyosarcoma patients, such as FGFR and CTLA4 inhibitory signaling. We validated the detected regulatory heterogeneity through analysis of networks and chromatin states in leiomyosarcoma cell lines. We showed that the heterogeneity identified with PORCUPINE is not associated with methylation profiles or clinical features, thereby suggesting an independent mechanism of patient heterogeneity driven by the complex landscape of gene regulatory interactions.
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Affiliation(s)
- Tatiana Belova
- Computational Biology and Systems Medicine Group, Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
| | - Nicola Biondi
- Precision Sarcoma Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases, Heidelberg, Germany
| | - Ping-Han Hsieh
- Computational Biology and Systems Medicine Group, Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Oncology, Catholic University (KU) Leuven, Leuven, Belgium
| | - Priya Chudasama
- Precision Sarcoma Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases, Heidelberg, Germany
| | - Marieke L Kuijjer
- Computational Biology and Systems Medicine Group, Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, the Netherlands
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24
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Dermawan JK, Rubin BP. The spectrum and significance of secondary (co-occurring) genetic alterations in sarcomas: the hallmarks of sarcomagenesis. J Pathol 2023; 260:637-648. [PMID: 37345731 DOI: 10.1002/path.6140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 06/23/2023]
Abstract
Bone and soft tissue tumors are generally classified into complex karyotype sarcomas versus those with recurrent genetic alterations, often in the form of gene fusions. In this review, we provide an overview of important co-occurring genomic alterations, organized by biological mechanisms and covering a spectrum of genomic alteration types: mutations (single-nucleotide variations or indels) in oncogenes or tumor suppressor genes, copy number alterations, transcriptomic signatures, genomic complexity indices (e.g. CINSARC), and complex genomic structural variants. We discuss the biological and prognostic roles of these so-called secondary or co-occurring alterations, arguing that recognition and detection of these alterations may be significant for our understanding and management of mesenchymal tumors. On a related note, we also discuss major recurrent alterations in so-called complex karyotype sarcomas. These secondary alterations are essential to sarcomagenesis via a variety of mechanisms, such as inactivation of tumor suppressors, activation of proliferative signal transduction, telomere maintenance, and aberrant regulation of epigenomic/chromatin remodeling players. The use of comprehensive genomic profiling, including targeted next-generation sequencing panels or whole-exome sequencing, may be incorporated into clinical workflows to offer more comprehensive, potentially clinically actionable information. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Josephine K Dermawan
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Brian P Rubin
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
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25
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Sarver AL, Mills LJ, Makielski KM, Temiz NA, Wang J, Spector LG, Subramanian S, Modiano JF. Distinct mechanisms of PTEN inactivation in dogs and humans highlight convergent molecular events that drive cell division in the pathogenesis of osteosarcoma. Cancer Genet 2023; 276-277:1-11. [PMID: 37267683 DOI: 10.1016/j.cancergen.2023.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/02/2023] [Accepted: 05/19/2023] [Indexed: 06/04/2023]
Abstract
A hallmark of osteosarcoma in both human and canine tumors is somatic fragmentation and rearrangement of chromosome structure which leads to recurrent increases and decreases in DNA copy number. The PTEN gene has been implicated as an important tumor suppressor in osteosarcoma via forward genetic screens. Here, we analyzed copy number changes, promoter methylation and transcriptomes to better understand the role of PTEN in canine and human osteosarcoma. Reduction in PTEN copy number was observed in 23 of 95 (25%) of the canine tumors examined leading to corresponding decreases in PTEN transcript levels from RNA-Seq samples. Unexpectedly, canine tumors with an intact PTEN locus had higher levels of PTEN transcripts than human tumors. This variation in transcript abundance was used to evaluate the role of PTEN in osteosarcoma biology. Decreased PTEN copy number and transcript level was observed in - and likely an important driver of - increases in cell cycle transcripts in four independent canine transcriptional datasets. In human osteosarcoma, homozygous copy number loss was not observed, instead increased methylation of the PTEN promoter was associated with increased cell cycle transcripts. Somatic modification of PTEN, either by homozygous deletion in dogs or by promoter methylation in humans, is clinically relevant to osteosarcoma, because the cell cycle related transcripts are associated with patient outcomes. The PTEN gene is part of a syntenic rearrangement unique to the canine genome, making it susceptible to somatic loss of both copies of distal chromosome 26 which also includes the FAS death receptor. SIGNIFICANCE STATEMENT: PTEN function is abrogated by different mechanisms in canine and human osteosarcoma tumors leading to uncontrolled cell cycling. Somatic loss of this canine specific syntenic region may help explain why the canine genome appears to be uniquely susceptible to osteosarcoma. Syntenic arrangement, in the context of copy number change, may lead to synergistic interactions that in turn modify species specific cancer risk. Comparative models of tumorigenesis may utilize different driver mechanisms.
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Affiliation(s)
- Aaron L Sarver
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA; Animal Cancer Care and Research Program, University of Minnesota, St. Paul, MN 55108, USA.
| | - Lauren J Mills
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Kelly M Makielski
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Animal Cancer Care and Research Program, University of Minnesota, St. Paul, MN 55108, USA; Department of Veterinary Clinical Sciences, University of Minnesota College of Veterinary Medicine, St. Paul, MN 55108, USA
| | - Nuri A Temiz
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jinhua Wang
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Logan G Spector
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN 55455, USA; Animal Cancer Care and Research Program, University of Minnesota, St. Paul, MN 55108, USA
| | - Subbaya Subramanian
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Animal Cancer Care and Research Program, University of Minnesota, St. Paul, MN 55108, USA; Department of Surgery, University of Minnesota School of Medicine, Minneapolis, MN 55455, USA
| | - Jaime F Modiano
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Animal Cancer Care and Research Program, University of Minnesota, St. Paul, MN 55108, USA; Department of Veterinary Clinical Sciences, University of Minnesota College of Veterinary Medicine, St. Paul, MN 55108, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA; Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Center for Engineering and Medicine, University of Minnesota, Minneapolis, MN 55455, USA; Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
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26
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Michot A, Lagarde P, Lesluyes T, Darbo E, Neuville A, Baud J, Perot G, Bonomo I, Maire M, Michot M, Coindre JM, Le Loarer F, Chibon F. Analysis of the Peritumoral Tissue Unveils Cellular Changes Associated with a High Risk of Recurrence. Cancers (Basel) 2023; 15:3450. [PMID: 37444560 DOI: 10.3390/cancers15133450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND The management of soft-tissue sarcoma (STS) relies on a multidisciplinary approach involving specialized oncological surgery combined with other adjuvant therapies to achieve optimal local disease control. Purpose and Results: Genomic and transcriptomic pseudocapsules of 20 prospective sarcomas were analyzed and revealed to be correlated with a higher risk of recurrence after surgery. CONCLUSIONS A peritumoral environment that has been remodeled and infiltrated by M2 macrophages, and is less expressive of healthy tissue, would pose a significant risk of relapse and require more aggressive treatment strategies.
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Affiliation(s)
- Audrey Michot
- Bordeaux Institute of Oncology, BRIC U1312, INSERM, 33000 Bordeaux, France
- Institut Bergonié, Centre de Lutte Contre le Cancer de Bordeaux, 33076 Bordeaux, France
- Department of Biopathology, Bergonié Institute, Université Victor Segalen Site Carreire, Bordeaux 2, 33076 Bordeaux, France
| | - Pauline Lagarde
- Institut Bergonié, Centre de Lutte Contre le Cancer de Bordeaux, 33076 Bordeaux, France
- Department of Biopathology, Bergonié Institute, Université Victor Segalen Site Carreire, Bordeaux 2, 33076 Bordeaux, France
| | - Tom Lesluyes
- Institut Bergonié, Centre de Lutte Contre le Cancer de Bordeaux, 33076 Bordeaux, France
| | - Elodie Darbo
- Bordeaux Institute of Oncology, BRIC U1312, INSERM, 33000 Bordeaux, France
- Department of Biopathology, Bergonié Institute, Université Victor Segalen Site Carreire, Bordeaux 2, 33076 Bordeaux, France
| | - Agnès Neuville
- Institut Bergonié, Centre de Lutte Contre le Cancer de Bordeaux, 33076 Bordeaux, France
| | - Jessica Baud
- Bordeaux Institute of Oncology, BRIC U1312, INSERM, 33000 Bordeaux, France
| | - Gaëlle Perot
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Iris Bonomo
- Institut Bergonié, Centre de Lutte Contre le Cancer de Bordeaux, 33076 Bordeaux, France
| | - Mathilde Maire
- Institut Bergonié, Centre de Lutte Contre le Cancer de Bordeaux, 33076 Bordeaux, France
| | - Maxime Michot
- Institut Bergonié, Centre de Lutte Contre le Cancer de Bordeaux, 33076 Bordeaux, France
| | - Jean-Michel Coindre
- Institut Bergonié, Centre de Lutte Contre le Cancer de Bordeaux, 33076 Bordeaux, France
- Department of Biopathology, Bergonié Institute, Université Victor Segalen Site Carreire, Bordeaux 2, 33076 Bordeaux, France
| | - François Le Loarer
- Bordeaux Institute of Oncology, BRIC U1312, INSERM, 33000 Bordeaux, France
- Institut Bergonié, Centre de Lutte Contre le Cancer de Bordeaux, 33076 Bordeaux, France
- Department of Biopathology, Bergonié Institute, Université Victor Segalen Site Carreire, Bordeaux 2, 33076 Bordeaux, France
| | - Frédéric Chibon
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
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27
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Burns J, Wilding CP, Krasny L, Zhu X, Chadha M, Tam YB, Ps H, Mahalingam AH, Lee ATJ, Arthur A, Guljar N, Perkins E, Pankova V, Jenks A, Djabatey V, Szecsei C, McCarthy F, Ragulan C, Milighetti M, Roumeliotis TI, Crosier S, Finetti M, Choudhary JS, Judson I, Fisher C, Schuster EF, Sadanandam A, Chen TW, Williamson D, Thway K, Jones RL, Cheang MCU, Huang PH. The proteomic landscape of soft tissue sarcomas. Nat Commun 2023; 14:3834. [PMID: 37386008 PMCID: PMC10310735 DOI: 10.1038/s41467-023-39486-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 06/15/2023] [Indexed: 07/01/2023] Open
Abstract
Soft tissue sarcomas (STS) are rare and diverse mesenchymal cancers with limited treatment options. Here we undertake comprehensive proteomic profiling of tumour specimens from 321 STS patients representing 11 histological subtypes. Within leiomyosarcomas, we identify three proteomic subtypes with distinct myogenesis and immune features, anatomical site distribution and survival outcomes. Characterisation of undifferentiated pleomorphic sarcomas and dedifferentiated liposarcomas with low infiltrating CD3 + T-lymphocyte levels nominates the complement cascade as a candidate immunotherapeutic target. Comparative analysis of proteomic and transcriptomic profiles highlights the proteomic-specific features for optimal risk stratification in angiosarcomas. Finally, we define functional signatures termed Sarcoma Proteomic Modules which transcend histological subtype classification and show that a vesicle transport protein signature is an independent prognostic factor for distant metastasis. Our study highlights the utility of proteomics for identifying molecular subgroups with implications for risk stratification and therapy selection and provides a rich resource for future sarcoma research.
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Affiliation(s)
- Jessica Burns
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | | | - Lukas Krasny
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Xixuan Zhu
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Madhumeeta Chadha
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Yuen Bun Tam
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Hari Ps
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | | | - Alexander T J Lee
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Amani Arthur
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Nafia Guljar
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Emma Perkins
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Valeriya Pankova
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Andrew Jenks
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Vanessa Djabatey
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Cornelia Szecsei
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Frank McCarthy
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Chanthirika Ragulan
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Martina Milighetti
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | | | - Stephen Crosier
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Martina Finetti
- Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Jyoti S Choudhary
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Ian Judson
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Cyril Fisher
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Eugene F Schuster
- Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden NHS Foundation Trust, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Anguraj Sadanandam
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Tom W Chen
- Department of Oncology, National Taiwan University Hospital, Taipei City, Taiwan
- Graduate Institute of Oncology, National Taiwan University College of Medicine Taipei, Taipei City, Taiwan
| | - Daniel Williamson
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Khin Thway
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Robin L Jones
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Maggie C U Cheang
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
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28
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Miallot R, Millet V, Groult Y, Modelska A, Crescence L, Roulland S, Henri S, Malissen B, Brouilly N, Panicot-Dubois L, Vincentelli R, Sulzenbacher G, Finetti P, Dutour A, Blay JY, Bertucci F, Galland F, Naquet P. An OMA1 redox site controls mitochondrial homeostasis, sarcoma growth, and immunogenicity. Life Sci Alliance 2023; 6:e202201767. [PMID: 37024121 PMCID: PMC10078952 DOI: 10.26508/lsa.202201767] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 04/08/2023] Open
Abstract
Aggressive tumors often display mitochondrial dysfunction. Upon oxidative stress, mitochondria undergo fission through OMA1-mediated cleavage of the fusion effector OPA1. In yeast, a redox-sensing switch participates in OMA1 activation. 3D modeling of OMA1 comforted the notion that cysteine 403 might participate in a similar sensor in mammalian cells. Using prime editing, we developed a mouse sarcoma cell line in which OMA1 cysteine 403 was mutated in alanine. Mutant cells showed impaired mitochondrial responses to stress including ATP production, reduced fission, resistance to apoptosis, and enhanced mitochondrial DNA release. This mutation prevented tumor development in immunocompetent, but not nude or cDC1 dendritic cell-deficient, mice. These cells prime CD8+ lymphocytes that accumulate in mutant tumors, whereas their depletion delays tumor control. Thus, OMA1 inactivation increased the development of anti-tumor immunity. Patients with complex genomic soft tissue sarcoma showed variations in the level of OMA1 and OPA1 transcripts. High expression of OPA1 in primary tumors was associated with shorter metastasis-free survival after surgery, and low expression of OPA1, with anti-tumor immune signatures. Targeting OMA1 activity may enhance sarcoma immunogenicity.
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Affiliation(s)
- Richard Miallot
- Aix-Marseille Université, INSERM, CNRS, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Virginie Millet
- Aix-Marseille Université, INSERM, CNRS, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Yann Groult
- Aix-Marseille Université, INSERM, CNRS, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Angelika Modelska
- Aix-Marseille Université, INSERM, CNRS, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Lydie Crescence
- Aix Marseille Université, INSERM 1263, INRAE 1260, Plateforme d'Imagerie Vasculaire et de Microscopie Intravitale, C2VN, Marseille, France
| | - Sandrine Roulland
- Aix-Marseille Université, INSERM, CNRS, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Sandrine Henri
- Aix-Marseille Université, INSERM, CNRS, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Bernard Malissen
- Aix-Marseille Université, INSERM, CNRS, Centre d'Immunologie de Marseille-Luminy, Marseille, France
- Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | | | - Laurence Panicot-Dubois
- Aix Marseille Université, INSERM 1263, INRAE 1260, Plateforme d'Imagerie Vasculaire et de Microscopie Intravitale, C2VN, Marseille, France
| | - Renaud Vincentelli
- Aix-Marseille Université, CNRS, Architecture et Fonction des Macromolécules Biologiques, Marseille, France
| | - Gerlind Sulzenbacher
- Aix-Marseille Université, CNRS, Architecture et Fonction des Macromolécules Biologiques, Marseille, France
| | - Pascal Finetti
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, Aix-Marseille Université, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Marseille, France
| | - Aurélie Dutour
- Childhood Cancers and Cell Death Laboratory, Cancer Research Center of Lyon (CRCL), INSERM 1052, CNRS, Lyon, France
| | - Jean-Yves Blay
- Childhood Cancers and Cell Death Laboratory, Cancer Research Center of Lyon (CRCL), INSERM 1052, CNRS, Lyon, France
- Department of Medicine, Centre Léon Bérard, UNICANCER & University Lyon I, Lyon, France
| | - François Bertucci
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, Aix-Marseille Université, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Marseille, France
| | - Franck Galland
- Aix-Marseille Université, INSERM, CNRS, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Philippe Naquet
- Aix-Marseille Université, INSERM, CNRS, Centre d'Immunologie de Marseille-Luminy, Marseille, France
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29
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Watson S, Gruel N, Le Loarer F. New developments in the pathology and molecular biology of retroperitoneal sarcomas. EUROPEAN JOURNAL OF SURGICAL ONCOLOGY 2023; 49:1053-1060. [PMID: 35151525 DOI: 10.1016/j.ejso.2022.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/22/2022] [Accepted: 02/02/2022] [Indexed: 02/07/2023]
Abstract
Retroperitoneal sarcomas (RPS) refer to a heterogeneous group of malignancies of mesenchymal origin developing from retroperitoneal tissues and vessels. The most frequent RPS are well differentiated/dedifferentiated liposarcomas and leiomyosarcomas, but other rare histological subtypes can be observed. Over the last decade, significant advances have been made in the pathological and molecular characterization of sarcomas. These advances have led to major changes in their diagnostic management as well as in the development of new therapeutic strategies based on tumor biology and microenvironment. This review describes the current knowledge and recent findings in the pathology and molecular biology of the most frequent RPS subtypes.
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Affiliation(s)
- Sarah Watson
- INSERM U830, Équipe Labellisée Ligue Nationale Contre le Cancer, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Center, Paris, France; Department of Medical Oncology, Institut Curie Hospital, Paris, France.
| | - Nadege Gruel
- INSERM U830, Équipe Labellisée Ligue Nationale Contre le Cancer, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Center, Paris, France; Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - François Le Loarer
- Department of Pathology, Institut Bergonie, Bordeaux, France; INSERM U1218, Unité ACTION, Institut Bergonie, Bordeaux, France; University of Bordeaux, Talence, France
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30
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Forker LJ, Bibby B, Yang L, Lane B, Irlam J, Mistry H, Khan M, Valentine H, Wylie J, Shenjere P, Leahy M, Gaunt P, Billingham L, Seddon BM, Grimer R, Robinson M, Choudhury A, West C. Technical development and validation of a clinically applicable microenvironment classifier as a biomarker of tumour hypoxia for soft tissue sarcoma. Br J Cancer 2023; 128:2307-2317. [PMID: 37085598 PMCID: PMC10241814 DOI: 10.1038/s41416-023-02265-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/09/2023] [Accepted: 03/28/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Soft tissue sarcomas (STS) are rare, heterogeneous tumours and biomarkers are needed to inform management. We previously derived a prognostic tumour microenvironment classifier (24-gene hypoxia signature). Here, we developed/validated an assay for clinical application. METHODS Technical performance of targeted assays (Taqman low-density array, nanoString) was compared in 28 prospectively collected formalin-fixed, paraffin-embedded (FFPE) biopsies. The nanoString assay was biologically validated by comparing to HIF-1α/CAIX immunohistochemistry (IHC) in clinical samples. The Manchester (n = 165) and VORTEX Phase III trial (n = 203) cohorts were used for clinical validation. The primary outcome was overall survival (OS). RESULTS Both assays demonstrated excellent reproducibility. The nanoString assay detected upregulation of the 24-gene signature under hypoxia in vitro, and 16/24 hypoxia genes were upregulated in tumours with high CAIX expression in vivo. Patients with hypoxia-high tumours had worse OS in the Manchester (HR 3.05, 95% CI 1.54-5.19, P = 0.0005) and VORTEX (HR 2.13, 95% CI 1.19-3.77, P = 0.009) cohorts. In the combined cohort, it was independently prognostic for OS (HR 2.24, 95% CI 1.42-3.53, P = 0.00096) and associated with worse local recurrence-free survival (HR 2.17, 95% CI 1.01-4.68, P = 0.04). CONCLUSIONS This study comprehensively validates a microenvironment classifier befitting FFPE STS biopsies. Future uses include: (1) selecting high-risk patients for perioperative chemotherapy; and (2) biomarker-driven trials of hypoxia-targeted therapies.
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Affiliation(s)
- Laura J Forker
- Translational Radiobiology Group, Division of Cancer Sciences, The Oglesby Cancer Research Building, The University of Manchester, Manchester Academic Health Science Centre, 555 Wilmslow Road, Manchester, M20 4GJ, UK.
- Department of Clinical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK.
| | - Becky Bibby
- Translational Radiobiology Group, Division of Cancer Sciences, The Oglesby Cancer Research Building, The University of Manchester, Manchester Academic Health Science Centre, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - Lingjian Yang
- Translational Radiobiology Group, Division of Cancer Sciences, The Oglesby Cancer Research Building, The University of Manchester, Manchester Academic Health Science Centre, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - Brian Lane
- Translational Radiobiology Group, Division of Cancer Sciences, The Oglesby Cancer Research Building, The University of Manchester, Manchester Academic Health Science Centre, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - Joely Irlam
- Translational Radiobiology Group, Division of Cancer Sciences, The Oglesby Cancer Research Building, The University of Manchester, Manchester Academic Health Science Centre, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - Hitesh Mistry
- Translational Radiobiology Group, Division of Cancer Sciences, The Oglesby Cancer Research Building, The University of Manchester, Manchester Academic Health Science Centre, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - Mairah Khan
- Translational Radiobiology Group, Division of Cancer Sciences, The Oglesby Cancer Research Building, The University of Manchester, Manchester Academic Health Science Centre, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - Helen Valentine
- Translational Radiobiology Group, Division of Cancer Sciences, The Oglesby Cancer Research Building, The University of Manchester, Manchester Academic Health Science Centre, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - James Wylie
- Department of Clinical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK
| | - Patrick Shenjere
- Department of Histopathology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK
| | - Michael Leahy
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK
| | - Piers Gaunt
- Cancer Research UK Clinical Trials Unit, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Lucinda Billingham
- Cancer Research UK Clinical Trials Unit, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Beatrice M Seddon
- Department of Oncology, University College London Hospitals NHS Foundation Trust, 1st Floor Central, 250 Euston Road, London, NW1 2PG, UK
| | - Rob Grimer
- Department of Orthopaedic Oncology, Royal Orthopaedic Hospital NHS Foundation Trust, Bristol Road South, Northfield, Birmingham, B31 2AP, UK
| | - Martin Robinson
- Department of Oncology, Academic Unit of Clinical Oncology (Cancer Clinical Trials Centre), Weston Park Hospital, Whitham Road, Sheffield, S10 2SJ, UK
| | - Ananya Choudhury
- Translational Radiobiology Group, Division of Cancer Sciences, The Oglesby Cancer Research Building, The University of Manchester, Manchester Academic Health Science Centre, 555 Wilmslow Road, Manchester, M20 4GJ, UK
- Department of Clinical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK
| | - Catharine West
- Translational Radiobiology Group, Division of Cancer Sciences, The Oglesby Cancer Research Building, The University of Manchester, Manchester Academic Health Science Centre, 555 Wilmslow Road, Manchester, M20 4GJ, UK
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31
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Kasper B, Baldi GG, Loong HHF, Trent J. EJSO educational Special issue from the TARPSWG - Standard medical treatment and new options in retroperitoneal sarcoma. EUROPEAN JOURNAL OF SURGICAL ONCOLOGY 2023; 49:1133-1139. [PMID: 34998634 DOI: 10.1016/j.ejso.2021.12.465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/20/2021] [Accepted: 12/25/2021] [Indexed: 01/10/2023]
Abstract
Retroperitoneal soft tissue sarcomas mainly consist histologically of liposarcomas and leiomyosarcomas. For the liposarcoma subgroup, the local relapse rate seems to determine patients' overall prognosis. In contrast, leiomyosarcoma patients are challenged by the development of metastatic disease; therefore, effective systemic therapies are the cornerstone to improve patients' outcome. No doubt, the limited number of active regimens currently available makes the treatment of patients with locally advanced and/or metastatic disease challenging and results in the overall poor prognosis of this population. In this European Journal of Surgical Oncology Educational Special Issue from the Transatlantic Australasian RetroPeritoneal Sarcoma Working Group (TARPSWG), we aim to summarize state-of-the-art systemic treatments for patients with retroperitoneal sarcomas with a focus on the locally advanced and metastatic disease setting including conventional standard chemotherapies as well as new innovative treatment approaches in order to identify current unmet medical needs guiding the sarcoma community to initiate appropriate translational research projects and design innovative clinical trials.
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Affiliation(s)
- Bernd Kasper
- University of Heidelberg, Mannheim University Medical Center, Sarcoma Unit, Mannheim, Germany.
| | | | - Herbert Ho-Fung Loong
- Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Jonathan Trent
- University of Miami, Sylvester Comprehensive Cancer Center, Miami, USA
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32
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Spalato-Ceruso M, Laroche-Clary A, Perret R, Valverde Y, Chaire V, Derieppe MA, Velasco V, Bourdon A, Italiano A. Genome-wide CRISPR/Cas9 library screening identified ATM signaling network genes as critical drivers for resistance to ATR inhibition in soft-tissue sarcomas: synthetic lethality and therapeutic implications. Exp Hematol Oncol 2023; 12:51. [PMID: 37259134 DOI: 10.1186/s40164-023-00416-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 05/16/2023] [Indexed: 06/02/2023] Open
Abstract
Soft-tissue sarcoma (STS) are a heterogeneous group of rare tumors with different biological behavior that are fatal in more than 40% of cases, due to their metastatic evolution and inadequate treatment options. ATR inhibition already showed an activity, even if modest, in broad pre-clinical models of STS. By using genome-wide CRISPR/Cas9 library screening, we identified ATM signaling network genes as critical drivers for resistance to the specific ATR inhibitor AZD6738. The role of such genes in resistance to AZD6738 was confirmed by using CRISPR/Cas9 knockout models. More strikingly, the ATM inhibitor AZD0156 works synergistically with AZD6738 in vitro and abolishes STS growth in vivo in our models of most frequent histotypes (such as dedifferentiated liposarcoma, leiomyosarcoma, and undifferentiated pleomorphic sarcoma among others). Moreover, the combination of AZD6738 and AZD0156 induced significantly higher levels of DNA damage than either drug used as single agent alone. In summary, our results demonstrate that targeting ATM is an effective approach to overcome resistance to ATR inhibition in different STS subtypes, including the most frequent histologies.
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Affiliation(s)
- M Spalato-Ceruso
- Sarcoma Unit, Institut Bergonié, 229 cours de l'Argonne, Bordeaux, 33000, France
- INSERM, U1312, Bordeaux, France
| | - A Laroche-Clary
- Sarcoma Unit, Institut Bergonié, 229 cours de l'Argonne, Bordeaux, 33000, France
- INSERM, U1312, Bordeaux, France
| | - R Perret
- Department of Pathology, Institut Bergonié, Bordeaux, France
| | - Y Valverde
- Sarcoma Unit, Institut Bergonié, 229 cours de l'Argonne, Bordeaux, 33000, France
- INSERM, U1312, Bordeaux, France
| | - V Chaire
- Sarcoma Unit, Institut Bergonié, 229 cours de l'Argonne, Bordeaux, 33000, France
- INSERM, U1312, Bordeaux, France
| | | | - V Velasco
- Department of Pathology, Institut Bergonié, Bordeaux, France
| | - A Bourdon
- Bioinformatics, Data and Digital Health Departement, Insitut Bergonié, Bordeaux, France
| | - A Italiano
- Sarcoma Unit, Institut Bergonié, 229 cours de l'Argonne, Bordeaux, 33000, France.
- INSERM, U1312, Bordeaux, France.
- University of Bordeaux, Bordeaux, France.
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33
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Villemin JP, Bassaganyas L, Pourquier D, Boissière F, Cabello-Aguilar S, Crapez E, Tanos R, Cornillot E, Turtoi A, Colinge J. Inferring ligand-receptor cellular networks from bulk and spatial transcriptomic datasets with BulkSignalR. Nucleic Acids Res 2023:7152875. [PMID: 37144485 DOI: 10.1093/nar/gkad352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/24/2023] [Accepted: 04/22/2023] [Indexed: 05/06/2023] Open
Abstract
The study of cellular networks mediated by ligand-receptor interactions has attracted much attention recently owing to single-cell omics. However, rich collections of bulk data accompanied with clinical information exists and continue to be generated with no equivalent in single-cell so far. In parallel, spatial transcriptomic (ST) analyses represent a revolutionary tool in biology. A large number of ST projects rely on multicellular resolution, for instance the Visium™ platform, where several cells are analyzed at each location, thus producing localized bulk data. Here, we describe BulkSignalR, a R package to infer ligand-receptor networks from bulk data. BulkSignalR integrates ligand-receptor interactions with downstream pathways to estimate statistical significance. A range of visualization methods complement the statistics, including functions dedicated to spatial data. We demonstrate BulkSignalR relevance using different datasets, including new Visium liver metastasis ST data, with experimental validation of protein colocalization. A comparison with other ST packages shows the significantly higher quality of BulkSignalR inferences. BulkSignalR can be applied to any species thanks to its built-in generic ortholog mapping functionality.
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Affiliation(s)
- Jean-Philippe Villemin
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
| | - Laia Bassaganyas
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
| | - Didier Pourquier
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
| | | | - Simon Cabello-Aguilar
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
| | - Evelyne Crapez
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
| | - Rita Tanos
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
| | - Emmanuel Cornillot
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
- Faculté de Pharmacie, Université de Montpellier, Montpellier, France
| | - Andrei Turtoi
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
| | - Jacques Colinge
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
- Faculté de Médecine, Université de Montpellier, Montpellier, France
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Li J, Zhou Q, Zhang C, Zhu H, Yao J, Zhang M. Development and validation of novel prognostic models for zinc finger proteins-related genes in soft tissue sarcoma. Aging (Albany NY) 2023; 15:3171-3190. [PMID: 37100454 DOI: 10.18632/aging.204682] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/15/2023] [Indexed: 04/28/2023]
Abstract
As the most common transcriptional regulators, zinc finer proteins (ZNFs) play vital roles in occurrence and progression of malignant tumors. Whereas, information regarding the roles of ZNFs in soft tissue sarcomas (STS) remains scarce. In this study, a comprehensive bioinformatics analysis investigating roles of ZNFs in STS was performed. Initially, we extracted raw datasets of differentially expressed ZNFs from GSE2719. Using a sequence of bioinformatics methods, we then investigated the prognostic significance, function, and molecular subtype of these differentially expressed ZNFs. In addition, CCK8 and plate clone formation assays were used to explore the effect of ZNF141 on STS cells. A total of 110 differentially expressed ZNFs were identified. Nine ZNFs (HLTF, ZNF292, ZNF141, LDB3, PHF14, ZNF322, PDLIM1, NR3C2, and LIMS2) were selected to establish an overall survival (OS) prediction model, and seven ZNFs (ZIC1, ZNF141, ZHX2, ZNF281, ZNHIT2, NR3C2, and LIMS2) were used to develop a progression-free survival (PFS) prediction model. Compared with patients with low-risk in the TCGA training and testing cohorts, as well as the GEO validation cohorts, patients with high-risk had poorer OS and PFS. Using nomograms constructed with the identified ZNFs predicting OS and PFS, we established a clinically useful model. Four distinct molecular subtypes with different prognostic and immune infiltration characteristics were identified. In vitro experiments showed that ZNF141 promoted the proliferation and viability of STS cells. In conclusion, ZNF-related models are useful as prognostic biomarkers, suggesting their potentials as therapeutic targets in STS. These findings will enable us to develop novel strategies treating STS, which will potentially improve outcomes of patients with STS.
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Affiliation(s)
- Junqing Li
- Minimally Invasive Spinal Surgery Center, Luoyang Orthopedic-Traumatological Hospital of Henan Province (Henan Provincial Orthopedic Hospital), Zhengzhou, China
| | - Quan Zhou
- Department of Orthopedics, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Henan University People’s Hospital, Zhengzhou, China
| | - Changsheng Zhang
- Minimally Invasive Spinal Surgery Center, Luoyang Orthopedic-Traumatological Hospital of Henan Province (Henan Provincial Orthopedic Hospital), Zhengzhou, China
| | - Huimin Zhu
- Minimally Invasive Spinal Surgery Center, Luoyang Orthopedic-Traumatological Hospital of Henan Province (Henan Provincial Orthopedic Hospital), Zhengzhou, China
| | - Jie Yao
- Minimally Invasive Spinal Surgery Center, Luoyang Orthopedic-Traumatological Hospital of Henan Province (Henan Provincial Orthopedic Hospital), Zhengzhou, China
| | - Meng Zhang
- Department of Orthopedics, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Henan University People’s Hospital, Zhengzhou, China
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Danieli M, Gronchi A. Staging Systems and Nomograms for Soft Tissue Sarcoma. Curr Oncol 2023; 30:3648-3671. [PMID: 37185391 PMCID: PMC10137294 DOI: 10.3390/curroncol30040278] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Reliable tools for prognosis prediction are crucially needed by oncologists so they can tailor individual treatments. However, the wide spectrum of histologies and prognostic behaviors of sarcomas challenges their development. In this field, nomograms could definitely better account for their granularity compared to the more widely used AJCC/UICC TNM staging system. Nomograms are predictive tools that incorporate multiple risk factors and return a numerical probability of a clinical event. Since the development of the first nomogram in 2002, several other nomograms have been built, either general, site-specific, histology-specific, or both. Recently, some new “dynamic” nomograms and prognostic tools have been developed, allowing doctors to “recalculate” a patient’s prognosis by taking into account the time since primary surgery, the event history, and the potential time-dependent effect of covariates. Due to these new tools, prognosis prediction is no longer limited to the time of the first computation but can be adapted and recalculated based on the occurrence (or not) of any event as time passes from the first computation. In this review, we aimed to give an overview of the available nomograms for STS and to help clinicians in the process of selecting the best tool for each patient.
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Crombé A, Matcuk GR, Fadli D, Sambri A, Patel DB, Paioli A, Kind M, Spinnato P. Role of Imaging in Initial Prognostication of Locally Advanced Soft Tissue Sarcomas. Acad Radiol 2023; 30:322-340. [PMID: 35534392 DOI: 10.1016/j.acra.2022.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/21/2022] [Accepted: 04/06/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND Although imaging is central in the initial staging of patients with soft tissue sarcomas (STS), it remains underused and few radiological features are currently used in practice for prognostication and to help guide the best therapeutic strategy. Yet, several prognostic qualitative and quantitative characteristics from magnetic resonance imaging (MRI) and positron emission tomography (PET) have been identified over these last decades. OBJECTIVE After an overview of the current validated prognostic features based on baseline imaging and their integration into prognostic tools, such as nomograms used by clinicians, the aim of this review is to summarize more complex and innovative MRI, PET, and radiomics features, and to highlight their role to predict indirectly (through histologic grade) or directly the patients' outcomes.
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Affiliation(s)
- Amandine Crombé
- Department of Diagnostic and Interventional Oncological Imaging, Institut Bergonié, Regional Comprehensive Cancer of Nouvelle-Aquitaine, 229, cours de l'Argonne, F-33076, Bordeaux, France; Department of musculoskeletal imaging, Pellegrin University Hospital, 2, place Amélie Raba-Léon, F-33000, Bordeaux, France; Models in Oncology (MONC) Team, INRIA Bordeaux Sud-Ouest, CNRS UMR 5251, Institut de Mathématiques de Bordeaux & Bordeaux University, 351 cours de la libération, F-33400 Talence, France.
| | - George R Matcuk
- Department of Imaging, Cedars-Sinai Medical Center, Los Angeles, California
| | - David Fadli
- Department of musculoskeletal imaging, Pellegrin University Hospital, 2, place Amélie Raba-Léon, F-33000, Bordeaux, France
| | - Andrea Sambri
- Alma Mater Studiorum, University of Bologna, Bologna, Italy; IRCCS Policlinico di Sant'Orsola, Bologna, Italy
| | - Dakshesh B Patel
- Department of Radiology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Anna Paioli
- Osteoncology Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Michele Kind
- Department of Diagnostic and Interventional Oncological Imaging, Institut Bergonié, Regional Comprehensive Cancer of Nouvelle-Aquitaine, 229, cours de l'Argonne, F-33076, Bordeaux, France
| | - Paolo Spinnato
- Diagnostic and Interventional Radiology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
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37
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Ballinger ML, Pattnaik S, Mundra PA, Zaheed M, Rath E, Priestley P, Baber J, Ray-Coquard I, Isambert N, Causeret S, van der Graaf WTA, Puri A, Duffaud F, Le Cesne A, Seddon B, Chandrasekar C, Schiffman JD, Brohl AS, James PA, Kurtz JE, Penel N, Myklebost O, Meza-Zepeda LA, Pickett H, Kansara M, Waddell N, Kondrashova O, Pearson JV, Barbour AP, Li S, Nguyen TL, Fatkin D, Graham RM, Giannoulatou E, Green MJ, Kaplan W, Ravishankar S, Copty J, Powell JE, Cuppen E, van Eijk K, Veldink J, Ahn JH, Kim JE, Randall RL, Tucker K, Judson I, Sarin R, Ludwig T, Genin E, Deleuze JF, Haber M, Marshall G, Cairns MJ, Blay JY, Thomas DM, Tattersall M, Neuhaus S, Lewis C, Tucker K, Carey-Smith R, Wood D, Porceddu S, Dickinson I, Thorne H, James P, Ray-Coquard I, Blay JY, Cassier P, Le Cesne A, Duffaud F, Penel N, Isambert N, Kurtz JE, Puri A, Sarin R, Ahn JH, Kim JE, Ward I, Judson I, van der Graaf W, Seddon B, Chandrasekar C, Rickar R, Hennig I, Schiffman J, Randall RL, Silvestri A, Zaratzian A, Tayao M, Walwyn K, Niedermayr E, Mang D, Clark R, Thorpe T, MacDonald J, Riddell K, Mar J, Fennelly V, Wicht A, Zielony B, Galligan E, Glavich G, Stoeckert J, Williams L, Djandjgava L, Buettner I, Osinki C, Stephens S, Rogasik M, Bouclier L, Girodet M, Charreton A, Fayet Y, Crasto S, Sandupatla B, Yoon Y, Je N, Thompson L, Fowler T, Johnson B, Petrikova G, Hambridge T, Hutchins A, Bottero D, Scanlon D, Stokes-Denson J, Génin E, Campion D, Dartigues JF, Deleuze JF, Lambert JC, Redon R, Ludwig T, Grenier-Boley B, Letort S, Lindenbaum P, Meyer V, Quenez O, Dina C, Bellenguez C, Le Clézio CC, Giemza J, Chatel S, Férec C, Le Marec H, Letenneur L, Nicolas G, Rouault K. Heritable defects in telomere and mitotic function selectively predispose to sarcomas. Science 2023; 379:253-260. [PMID: 36656928 DOI: 10.1126/science.abj4784] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 11/16/2022] [Indexed: 01/20/2023]
Abstract
Cancer genetics has to date focused on epithelial malignancies, identifying multiple histotype-specific pathways underlying cancer susceptibility. Sarcomas are rare malignancies predominantly derived from embryonic mesoderm. To identify pathways specific to mesenchymal cancers, we performed whole-genome germline sequencing on 1644 sporadic cases and 3205 matched healthy elderly controls. Using an extreme phenotype design, a combined rare-variant burden and ontologic analysis identified two sarcoma-specific pathways involved in mitotic and telomere functions. Variants in centrosome genes are linked to malignant peripheral nerve sheath and gastrointestinal stromal tumors, whereas heritable defects in the shelterin complex link susceptibility to sarcoma, melanoma, and thyroid cancers. These studies indicate a specific role for heritable defects in mitotic and telomere biology in risk of sarcomas.
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Affiliation(s)
- Mandy L Ballinger
- Garvan Institute of Medical Research, Sydney 2010, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney 2010, Australia
| | - Swetansu Pattnaik
- Garvan Institute of Medical Research, Sydney 2010, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney 2010, Australia
| | - Piyushkumar A Mundra
- Garvan Institute of Medical Research, Sydney 2010, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney 2010, Australia
| | - Milita Zaheed
- Hereditary Cancer Centre, Prince of Wales Hospital, Sydney 2031, Australia
| | - Emma Rath
- Garvan Institute of Medical Research, Sydney 2010, Australia
| | - Peter Priestley
- Hartwig Medical Foundation, 1098 XH Amsterdam, Netherlands
- Hartwig Medical Foundation Australia, Sydney 2000, Australia
| | - Jonathan Baber
- Hartwig Medical Foundation, 1098 XH Amsterdam, Netherlands
- Hartwig Medical Foundation Australia, Sydney 2000, Australia
| | - Isabelle Ray-Coquard
- Department of Adult Medical Oncology, Centre Leon Berard, University Claude Bernard, 69373 Lyon, France
| | | | | | | | - Ajay Puri
- Department of Orthopedic Oncology, Tata Memorial Hospital, Mumbai, Maharashtra 400012, India
| | | | | | - Beatrice Seddon
- Sarcoma Unit, University College Hospital, London NW1 2BU, UK
| | | | - Joshua D Schiffman
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Andrew S Brohl
- Sarcoma Department, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Paul A James
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne 3010, Australia
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne 3000, Australia
| | | | | | - Ola Myklebost
- Western Norway Familial Cancer Centre, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Science, University of Bergen, 5007 Bergen, Norway
- Institute for Cancer Research, Oslo University Hospital, N-0424 Oslo, Norway
| | | | - Hilda Pickett
- Children's Medical Research Institute, The University of Sydney, Westmead 2145, Australia
| | - Maya Kansara
- Garvan Institute of Medical Research, Sydney 2010, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney 2010, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane 4006, Australia
| | - Olga Kondrashova
- QIMR Berghofer Medical Research Institute, Brisbane 4006, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Brisbane 4006, Australia
| | - Andrew P Barbour
- Faculty of Medicine. The University of Queensland, Brisbane 4072, Australia
| | - Shuai Li
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne 3010, Australia
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton 3800, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville 3051, Australia
| | - Tuong L Nguyen
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne 3010, Australia
| | - Diane Fatkin
- St Vincent's Clinical School, University of New South Wales, Sydney 2010, Australia
- Molecular Cardiology Division, Victor Chang Cardiac Research Institute, Darlinghurst 2010, Australia
- Cardiology Department, St Vincent's Hospital, Sydney 2010, Australia
| | - Robert M Graham
- St Vincent's Clinical School, University of New South Wales, Sydney 2010, Australia
- Molecular Cardiology Division, Victor Chang Cardiac Research Institute, Darlinghurst 2010, Australia
| | - Eleni Giannoulatou
- St Vincent's Clinical School, University of New South Wales, Sydney 2010, Australia
- Computational Genomics Division, Victor Chang Cardiac Research Institute, Sydney 2010, Australia
| | - Melissa J Green
- School of Psychiatry, University of New South Wales, Sydney 2052, Australia
- Neuorscience Research Australia, Sydney 2031, Australia
| | - Warren Kaplan
- Garvan Institute of Medical Research, Sydney 2010, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney 2010, Australia
| | | | - Joseph Copty
- Garvan Institute of Medical Research, Sydney 2010, Australia
| | - Joseph E Powell
- Garvan Institute of Medical Research, Sydney 2010, Australia
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney 2052, Australia
| | - Edwin Cuppen
- Hartwig Medical Foundation, 1098 XH Amsterdam, Netherlands
| | - Kristel van Eijk
- Department of Neurology, University Medical Centre Utrecht Brain Center, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Jan Veldink
- Department of Neurology, University Medical Centre Utrecht Brain Center, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Jin-Hee Ahn
- Department of Oncology, Asan Medical Centre, Seoul 05505, South Korea
| | - Jeong Eun Kim
- Department of Oncology, Asan Medical Centre, Seoul 05505, South Korea
| | - R Lor Randall
- Department of Orthopaedic Surgery, University of California, Davis Health, Sacramento, CA 95817, USA
| | - Kathy Tucker
- Hereditary Cancer Centre, Prince of Wales Hospital, Sydney 2031, Australia
| | - Ian Judson
- Sarcoma Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Rajiv Sarin
- Cancer Genetics Unit, ACTREC, Tata Memorial Centre, Mumbai, Maharashtra 410210, India
| | - Thomas Ludwig
- Université de Brest, Inserm, EFS, UMR 1078, GGB, CHU de Brest, 29200 Brest, France
| | - Emmanuelle Genin
- Université de Brest, Inserm, EFS, UMR 1078, GGB, CHU de Brest, 29200 Brest, France
| | - Jean-Francois Deleuze
- Centre National de Recherche en Génomique Humaine, Institut de Génomique, 91057 Evry, France
| | - Michelle Haber
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Kensington 2033, Australia
| | - Glenn Marshall
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Kensington 2033, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick 2031, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan 2308, Australia
- Centre for Brain and Mental Health Research, The Hunter Medical Research Institute, Newcastle 2305, Australia
| | - Jean-Yves Blay
- Department of Adult Medical Oncology, Centre Leon Berard, University Claude Bernard, 69373 Lyon, France
| | - David M Thomas
- Garvan Institute of Medical Research, Sydney 2010, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney 2010, Australia
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38
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Darbo E, Pérot G, Darmusey L, Le Guellec S, Leroy L, Gaston L, Desplat N, Thébault N, Merle C, Rochaix P, Valentin T, Ferron G, Chevreau C, Bui B, Stoeckle E, Ranchere-Vince D, Méeus P, Terrier P, Piperno-Neumann S, Collin F, De Pinieux G, Duffaud F, Coindre JM, Blay JY, Chibon F. Distinct Cellular Origins and Differentiation Process Account for Distinct Oncogenic and Clinical Behaviors of Leiomyosarcomas. Cancers (Basel) 2023; 15:cancers15020534. [PMID: 36672483 PMCID: PMC9856933 DOI: 10.3390/cancers15020534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/02/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
In leiomyosarcoma (LMS), a very aggressive disease, a relatively transcriptionally uniform subgroup of well-differentiated tumors has been described and is associated with poor survival. The question raised how differentiation and tumor progression, two apparently antagonist processes, coexist and allow tumor malignancy. We first identified the most transcriptionally homogeneous LMS subgroup in three independent cohorts, which we named 'hLMS'. The integration of multi-omics data and functional analysis suggests that hLMS originate from vascular smooth muscle cells and show that hLMS transcriptional program reflects both modulations of smooth muscle contraction activity controlled by MYOCD/SRF regulatory network and activation of the cell cycle activity controlled by E2F/RB1 pathway. We propose that the phenotypic plasticity of vascular smooth muscle cells coupled with MYOCD/SRF pathway amplification, essential for hLMS survival, concomitant with PTEN absence and RB1 alteration, could explain how hLMS balance this uncommon interplay between differentiation and aggressiveness.
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Affiliation(s)
- Elodie Darbo
- INSERM U1218 ACTION, Institut Bergonié, 33000 Bordeaux, France
- CNRS UMR5800, LaBRI, 33400 Talence, France
- Department of Medical and Biological Sciences, Université de Bordeaux, 33000 Bordeaux, France
| | - Gaëlle Pérot
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Centre Hospitalier Universitaire (CHU) de Toulouse, IUCT-Oncopole, 31000 Toulouse, France
| | - Lucie Darmusey
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
- Department of Medical and Biological Sciences, University of Toulouse 3, 31000 Toulouse, France
| | - Sophie Le Guellec
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Laura Leroy
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Laëtitia Gaston
- Department of Medical Genetics, CHU de Bordeaux, 33000 Bordeaux, France
| | - Nelly Desplat
- INSERM U1218 ACTION, Institut Bergonié, 33000 Bordeaux, France
| | - Noémie Thébault
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Candice Merle
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
- Department of Medical and Biological Sciences, University of Toulouse 3, 31000 Toulouse, France
| | - Philippe Rochaix
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Thibaud Valentin
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Oncology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Gwenaël Ferron
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Surgical Oncology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Christine Chevreau
- Department of Oncology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Binh Bui
- Department of Oncology, Institut Bergonié, 33000 Bordeaux, France
| | | | | | - Pierre Méeus
- Department of Surgery, Centre Léon Bérard, 69000 Lyon, France
| | - Philippe Terrier
- Department of Pathology, Institut Gustave Roussy, 94800 Villejuif, France
| | | | - Françoise Collin
- Department of Pathology, Centre Georges-François Leclerc, 21000 Dijon, France
| | - Gonzague De Pinieux
- Department of Pathology, Hôpital Universitaire Trousseau, 37170 Tours, France
| | - Florence Duffaud
- Medical Oncology Unit, APHM Hôpital La Timone, Aix Marseille University, 13000 Marseille, France
| | - Jean-Michel Coindre
- INSERM U1218 ACTION, Institut Bergonié, 33000 Bordeaux, France
- Department of Pathology, Institut Bergonié, 33000 Bordeaux, France
| | - Jean-Yves Blay
- Department of Medical Oncology, Centre Léon Bérard, 69000 Lyon, France
- INSERM U1052, CNRS 5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, 69000 Lyon, France
| | - Frédéric Chibon
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
- Correspondence: ; Tel.: +33-0582741765
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Connolly EA, Grimison PS, Horvath LG, Robinson PJ, Reddel RR. Quantitative proteomic studies addressing unmet clinical needs in sarcoma. Front Oncol 2023; 13:1126736. [PMID: 37197427 PMCID: PMC10183589 DOI: 10.3389/fonc.2023.1126736] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 03/31/2023] [Indexed: 05/19/2023] Open
Abstract
Sarcoma is a rare and complex disease comprising over 80 malignant subtypes that is frequently characterized by poor prognosis. Challenges in clinical management include uncertainties in diagnosis and disease classification, limited prognostic and predictive biomarkers, incompletely understood disease heterogeneity among and within subtypes, lack of effective treatment options, and limited progress in identifying new drug targets and novel therapeutics. Proteomics refers to the study of the entire complement of proteins expressed in specific cells or tissues. Advances in proteomics have included the development of quantitative mass spectrometry (MS)-based technologies which enable analysis of large numbers of proteins with relatively high throughput, enabling proteomics to be studied on a scale that has not previously been possible. Cellular function is determined by the levels of various proteins and their interactions, so proteomics offers the possibility of new insights into cancer biology. Sarcoma proteomics therefore has the potential to address some of the key current challenges described above, but it is still in its infancy. This review covers key quantitative proteomic sarcoma studies with findings that pertain to clinical utility. Proteomic methodologies that have been applied to human sarcoma research are briefly described, including recent advances in MS-based proteomic technology. We highlight studies that illustrate how proteomics may aid diagnosis and improve disease classification by distinguishing sarcoma histologies and identify distinct profiles within histological subtypes which may aid understanding of disease heterogeneity. We also review studies where proteomics has been applied to identify prognostic, predictive and therapeutic biomarkers. These studies traverse a range of histological subtypes including chordoma, Ewing sarcoma, gastrointestinal stromal tumors, leiomyosarcoma, liposarcoma, malignant peripheral nerve sheath tumors, myxofibrosarcoma, rhabdomyosarcoma, synovial sarcoma, osteosarcoma, and undifferentiated pleomorphic sarcoma. Critical questions and unmet needs in sarcoma which can potentially be addressed with proteomics are outlined.
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Affiliation(s)
- Elizabeth A. Connolly
- ProCan, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
- Department of Medical Oncology, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- *Correspondence: Elizabeth A. Connolly,
| | - Peter S. Grimison
- Department of Medical Oncology, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Lisa G. Horvath
- Department of Medical Oncology, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Phillip J. Robinson
- ProCan, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Roger R. Reddel
- ProCan, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
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40
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Crombé A, Kind M, Fadli D, Miceli M, Linck PA, Bianchi G, Sambri A, Spinnato P. Soft-tissue sarcoma in adults: Imaging appearances, pitfalls and diagnostic algorithms. Diagn Interv Imaging 2022; 104:207-220. [PMID: 36567193 DOI: 10.1016/j.diii.2022.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
This article provides an overview of the current knowledge regarding diagnostic imaging of patients with soft-tissue sarcomas, which is a heterogeneous group of rare mesenchymal malignancies. After an initial contextualization, diagnostic flow-chart based on initial radiological findings of soft-tissue masses (with specific focus on adipocytic soft-tissue tumors [STTs], hemorragic STTs and retroperitoneal STTs) are provided considering relevant results from novel researches, guidelines, and experts' viewpoints, with the aim to help radiologists and clinicians in their practice. Particularly, the central place of sarcoma reference centers in the diagnostic and therapeutic management is highlighted, as well as the pivotal role that radiologists should play to correctly identify patients with soft-tissue sarcoma at the initial stage of the disease. Indications and methods for performing imaging-guided biopsies are also discussed, as well as clues to improve soft-tissue sarcoma grading with conventional and quantitative imaging.
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Affiliation(s)
- Amandine Crombé
- Department of Musculoskeletal Imaging, Pellegrin University Hospital, Bordeaux 33076, France; Department of Diagnostic and Interventional Oncological Imaging, Institut Bergonié, Regional Comprehensive Cancer of Nouvelle-Aquitaine, Bordeaux 33076, France; Models in Oncology (MONC) Team, INRIA Bordeaux Sud-Ouest, CNRS UMR 5251 & Bordeaux University, 33400 Talence, France.
| | - Michèle Kind
- Department of Diagnostic and Interventional Oncological Imaging, Institut Bergonié, Regional Comprehensive Cancer of Nouvelle-Aquitaine, Bordeaux 33076, France
| | - David Fadli
- Department of Musculoskeletal Imaging, Pellegrin University Hospital, Bordeaux 33076, France
| | - Marco Miceli
- Diagnostic and Interventional Radiology, IRCCS Istituto Ortopedico Rizzoli, Bologna 40136, Italy
| | - Pierre-Antoine Linck
- Department of Diagnostic and Interventional Oncological Imaging, Institut Bergonié, Regional Comprehensive Cancer of Nouvelle-Aquitaine, Bordeaux 33076, France
| | - Giuseppe Bianchi
- Orthopedic Musculoskeletal Oncology Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna 40136, Italy
| | - Andrea Sambri
- Orthopedics and Traumatology Department, IRCCS Azienda Ospedaliero Universitaria di Bologna, Via Massarenti 9, Bologna 40138, Italy
| | - Paolo Spinnato
- Diagnostic and Interventional Radiology, IRCCS Istituto Ortopedico Rizzoli, Bologna 40136, Italy
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41
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Beebe E, Pöschel A, Kunz L, Wolski W, Motamed Z, Meier D, Guscetti F, Nolff MC, Markkanen E. Proteomic profiling of canine fibrosarcoma and adjacent peritumoral tissue. Neoplasia 2022; 35:100858. [PMID: 36508875 PMCID: PMC9761855 DOI: 10.1016/j.neo.2022.100858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
Fibrosarcoma (FSA) are rare soft tissue tumors that display aggressive local behavior and invasive growth leading to high rates of tumor recurrence. While the low incidence in humans hampers detailed understanding of the disease, FSA are frequent in dogs and present potential models for the human condition. However, a lack of in-depth molecular characterization of FSA and unaffected peritumoral tissue (PTT) in both species impedes the translational potential of dogs. To address this shortcoming, we characterized canine FSA and matched skeletal muscle, adipose and connective tissue using laser-capture microdissection (LCM) and LC-MS/MS in 30 formalin-fixed paraffin embedded (FFPE) specimens. Principal component analysis of 3'530 different proteins detected across all samples clearly separates the four tissues, with several targets strongly differentiating tumor from all three PTTs. 25 proteins were exclusively found in tumor tissue in ≥80% of cases. Among these, CD68 (a macrophage marker), Optineurin (OPTN), Nuclear receptor coactivator 5 (NCOA5), RAP1GDS1 (Rap1 GTPase-GDP dissociation stimulator 1) and Stromal cell derived factor 2 like 1 (SDF2L1) were present in ≥90% of FSA. Protein expression across all FSA was highly homogeneous and characterized by MYC and TP53 signaling, hyperactive EIF2 and immune-related changes as well as strongly decreased oxidative phosphorylation and oxidative lipid metabolism. Finally, we demonstrate significant molecular homology between canine FSA and human soft-tissue sarcomas, emphasizing the relevance of studying canine FSA as a model for human FSA. In conclusion, we provide the first detailed overview of proteomic changes in FSA and surrounding PTT with relevance for the human disease.
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Affiliation(s)
- Erin Beebe
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, 8057 Zürich, Switzerland
| | - Amiskwia Pöschel
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, 8057 Zürich, Switzerland
| | - Laura Kunz
- Functional Genomics Center Zürich, ETH Zürich/University of Zurich, 8057 Zürich, Switzerland
| | - Witold Wolski
- Functional Genomics Center Zürich, ETH Zürich/University of Zurich, 8057 Zürich, Switzerland
| | - Zahra Motamed
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, 8057 Zürich, Switzerland
| | - Daniela Meier
- Zyto/Histo Diagnostik Labor Freienstein, 8427 Freienstein, Switzerland
| | - Franco Guscetti
- Institute of Veterinary Pathology Vetsuisse Faculty, University of Zurich, 8057 Zürich, Switzerland
| | - Mirja C. Nolff
- Small Animal Surgery, Tierspital Zürich, 8057 Zürich, Switzerland,Corresponding authors.
| | - Enni Markkanen
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, 8057 Zürich, Switzerland,Corresponding authors.
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42
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Brunac AC, Fourquet J, Perot G, Jaffrelot M, Meilleroux J, Danjoux M, Filleron T, Nicolaï V, Guimbaud R, Icher S, Farés N, Selves J, Chibon F. CINSARC signature outperforms gold-standard TNM staging and consensus molecular subtypes for clinical outcome in stage II-III colorectal carcinoma. Mod Pathol 2022; 35:2002-2010. [PMID: 36202996 DOI: 10.1038/s41379-022-01166-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 12/24/2022]
Abstract
The outcome of stage II-III colorectal cancer (CRC) is highly variable and therapeutic choice is currently based on TNM staging with a few additional biomarkers. However, studies show that some stage III patients have a better prognosis than some stage II patients. A promising consensus molecular (CMS) classification with prognostic relevance has been developed, but it is not used in daily practice. Our team developed CINSARC, a 67-gene expression prognostic signature, whose prognostic value has been demonstrated in many cancer types. It is applicable to formalin-fixed, paraffin-embedded (FFPE) blocks using NanoString® technology. We investigated whether it could predict outcome in stage II-III CRC. We established the CINSARC classification on the TCGA retrospective cohort comprising 297 stage II-III CRC patients using RNA sequencing and on a second independent cohort comprising 169 cases using NanoString® technology. We compared its recurrence-free and overall survival prognostic value with TNM staging and CMS classification. In the TCGA cohort, we showed that CINSARC significantly splits the population of stage II-III CRC into two groups with different progression-free interval (P = 1.68 × 10-2; HR = 1.87 [1.11-3.16]) and overall survival (P = 3.73 × 10-3; HR = 2.45 [1.31-4.59]) and is a strong prognostic factor in multivariate analysis, outperforming TNM staging and CMS classification. We validated these results in the second cohort by applying CINSARC on FFPE samples with Nanostring® technology. CINSARC is a ready-to-use tool with a robust independent prognostic value in stage II-III CRC.
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Affiliation(s)
- Anne-Cécile Brunac
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Joanna Fourquet
- Oncogenesis of Sarcomas, INSERM UMR1037, Cancer Research Centre of Toulouse, Toulouse, France
| | - Gaëlle Perot
- Oncogenesis of Sarcomas, INSERM UMR1037, Cancer Research Centre of Toulouse, Toulouse, France
| | - Marion Jaffrelot
- Department of Digestive Oncology, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Julie Meilleroux
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Marie Danjoux
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Thomas Filleron
- Department of Biostatistics, Institut Claudius-Regaud, Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
| | - Vincent Nicolaï
- Department of Medical Oncology, Institut Universitaire du Cancer-Oncopole de Toulouse, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Rosine Guimbaud
- Department of Digestive Oncology, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Samira Icher
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Nadim Farés
- Department of Digestive Oncology, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Janick Selves
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Frédéric Chibon
- Oncogenesis of Sarcomas, INSERM UMR1037, Cancer Research Centre of Toulouse, Toulouse, France.
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43
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Crombé A, Roulleau‐Dugage M, Italiano A. The diagnosis, classification, and treatment of sarcoma in this era of artificial intelligence and immunotherapy. CANCER COMMUNICATIONS (LONDON, ENGLAND) 2022; 42:1288-1313. [PMID: 36260064 PMCID: PMC9759765 DOI: 10.1002/cac2.12373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 09/20/2022] [Accepted: 10/08/2022] [Indexed: 01/25/2023]
Abstract
Soft-tissue sarcomas (STS) represent a group of rare and heterogeneous tumors associated with several challenges, including incorrect or late diagnosis, the lack of clinical expertise, and limited therapeutic options. Digital pathology and radiomics represent transformative technologies that appear promising for improving the accuracy of cancer diagnosis, characterization and monitoring. Herein, we review the potential role of the application of digital pathology and radiomics in managing patients with STS. We have particularly described the main results and the limits of the studies using radiomics to refine diagnosis or predict the outcome of patients with soft-tissue sarcomas. We also discussed the current limitation of implementing radiomics in routine settings. Standard management approaches for STS have not improved since the early 1970s. Immunotherapy has revolutionized cancer treatment; nonetheless, immuno-oncology agents have not yet been approved for patients with STS. However, several lines of evidence indicate that immunotherapy may represent an efficient therapeutic strategy for this group of diseases. Thus, we emphasized the remarkable potential of immunotherapy in sarcoma treatment by focusing on recent data regarding the immune landscape of these tumors. We have particularly emphasized the fact that the development of immunotherapy for sarcomas is not an aspect of histology (except for alveolar soft-part sarcoma) but rather that of the tumor microenvironment. Future studies investigating immunotherapy strategies in sarcomas should incorporate at least the presence of tertiary lymphoid structures as a stratification factor in their design, besides including a strong translational program that will allow for a better understanding of the determinants involved in sensitivity and treatment resistance to immune-oncology agents.
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Affiliation(s)
- Amandine Crombé
- Department of ImagingInstitut BergoniéBordeauxNouvelle‐AquitaineF‐33076France,Faculty of MedicineUniversity of BordeauxBordeauxNouvelle‐AquitaineF‐33000France
| | | | - Antoine Italiano
- Faculty of MedicineUniversity of BordeauxBordeauxNouvelle‐AquitaineF‐33000France,Early Phase Trials and Sarcoma UnitInstitut BergoniéBordeauxNouvelle‐AquitaineF‐33076France
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Boudin L, de Nonneville A, Finetti P, Mescam L, Le Cesne A, Italiano A, Blay JY, Birnbaum D, Mamessier E, Bertucci F. CSPG4 expression in soft tissue sarcomas is associated with poor prognosis and low cytotoxic immune response. Lab Invest 2022; 20:464. [PMID: 36221119 PMCID: PMC9552405 DOI: 10.1186/s12967-022-03679-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 09/29/2022] [Indexed: 11/10/2022]
Abstract
Background Soft tissue sarcomas (STS) are heterogeneous and pro-metastatic tumors. Identification of accurate prognostic factors and novel therapeutic targets are crucial. CSPG4 is a cell surface proteoglycan with oncogenic functions. It recently emerged as a potential target for immunotherapy, including cell therapy based on CSPG4-specific chimeric antigen receptor (CAR)-redirected cytokine-induced killer lymphocytes (CSPG4-CAR.CIKs) in STS. However, expression of CSPG4 is poorly known in STS so far. Methods We analyzed CSPG4 gene expression in 1378 localized STS clinical samples, and searched for correlations with clinicopathological data, including disease-free survival (DFS), and with tumor immune features. Results CSPG4 expression was heterogeneous across samples. High expression was associated with younger patients’ age, more frequent undifferentiated pleomorphic sarcoma and myxofibrosarcoma pathological subtypes, more frequent internal trunk tumor site, and more CINSARC high-risk samples. No correlation existed with pathological tumor size and grade, and tumor depth. Patients with high CSPG4 expression displayed 49% (95% CI 42–57) 5-year DFS versus 61% (95% CI 56–68) in patients with low expression (p = 3.17E−03), representing a 49% increased risk of event in the “CSPG4-high” group (HR = 1.49, 95% CI 1.14–1.94). This unfavorable prognostic value persisted in multivariate analysis, independently from other variables. There were significant differences in immune variables between “CSPG4-high” and “CSPG4-low” tumors. The "CSPG4-low" tumors displayed profiles suggesting higher anti-tumor cytotoxic immune response and higher potential vulnerability to immune checkpoint inhibitors (ICI). By contrast, the "CSPG4-high" tumors displayed profiles implying an immune-excluded tumor microenvironment, potentially induced by hypoxia, resulting from an immature chaotic microvasculature, and/or the presence of contractile myofibroblasts. Conclusions Patients with “CSPG4-high” STS, theoretically candidate for CAR.CIKs, display shorter DFS and an immune environment unfavorable to vulnerability to CAR.CIKs, which could be improved by combining anti-angiogenic drugs able to normalize the tumor vasculature. By contrast, “CSPG4-low” STS are better candidates for immune therapy involving ICI. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03679-y.
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Affiliation(s)
- Laurys Boudin
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, INSERM UMR1068, CNRS UMR725, Marseille, France
| | - A de Nonneville
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, INSERM UMR1068, CNRS UMR725, Marseille, France.,Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Pascal Finetti
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, INSERM UMR1068, CNRS UMR725, Marseille, France
| | - Léna Mescam
- French Sarcoma Group, Lyon, France.,Department of Pathology, Institut Paoli-Calmettes, 232 Bd. Sainte-Marguerite, 13009, Marseille, France
| | - A Le Cesne
- French Sarcoma Group, Lyon, France.,Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Antoine Italiano
- French Sarcoma Group, Lyon, France.,Department of Medical Oncology, Institut Bergonie, Bordeaux, France
| | - Jean-Yves Blay
- French Sarcoma Group, Lyon, France.,Department of Medical Oncology, Centre Léon Bérard, UNICANCER &, Université Claude Bernard Lyon I, Lyon, France
| | - Daniel Birnbaum
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, INSERM UMR1068, CNRS UMR725, Marseille, France
| | - Emilie Mamessier
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, INSERM UMR1068, CNRS UMR725, Marseille, France
| | - François Bertucci
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, INSERM UMR1068, CNRS UMR725, Marseille, France. .,Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France. .,French Sarcoma Group, Lyon, France.
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45
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Weng W, Yu L, Li Z, Tan C, Lv J, Lao IW, Hu W, Deng Z, Liu Z, Wang J, Xu M. The immune subtypes and landscape of sarcomas. BMC Immunol 2022; 23:46. [PMID: 36153483 PMCID: PMC9508767 DOI: 10.1186/s12865-022-00522-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/14/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Considering the molecular heterogeneity of sarcomas and their immunologically quiet character, immunotherapy (e.g., immune checkpoint inhibitors) plays a viable role in only a subset of these tumors. This study aimed to determine the immune subtypes (IMSs) of sarcomas for selecting suitable patients from an extremely heterogeneous population.
Results
By performing consensus clustering analysis of the gene expression profiles of 538 patients with sarcomas in online databases, we stratified sarcomas into three IMSs characterized by different immune cell features, tumor mutational burdens (TMBs), gene mutations, and clinical outcomes. IMS1 showed an immune “hot” and immunosuppressive phenotype, the highest frequencies of CSMD3 mutation but the lowest frequencies of HMCN1 and LAMA2 mutations; these patients had the worst progression-free survival (PFS). IMS2 was defined by a high TMB and more gene mutations, but had the lowest frequency of MND1 mutations. IMS3 displayed the highest MDN1 expression level and an immune “cold” phenotype, these patients had the worst PFS. Each subtype was associated with different expression levels of immunogenic cell death modulators and immune checkpoints. Moreover, we applied graph learning-based dimensionality reduction to the immune landscape and identified significant intra-cluster heterogeneity within each IMS. Finally, we developed and validated an immune gene signature with good prognostic performance.
Conclusions
Our results provide a conceptual framework for understanding the immunological heterogeneity of sarcomas. The identification of immune-related subtypes may facilitate optimal selection of sarcoma patients who will respond to appropriate therapeutic strategies.
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46
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Sun Z, Yin M, Ding Y, Zhu Z, Sun Y, Li K, Yan W. Integrative analysis of synovial sarcoma transcriptome reveals different types of transcriptomic changes. Front Genet 2022; 13:925564. [PMID: 36118864 PMCID: PMC9478865 DOI: 10.3389/fgene.2022.925564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Synovial sarcoma (SS) is a rare and aggressive cancer that can come from distinct soft tissue types including muscle and ligaments. However, the transcriptomic landscape of SS is still poorly understood. This study aimed to systematically dissect the changes in SS transcriptome from different perspectives.Methods: We performed deep total RNA sequencing on ten paired Synovial sarcoma and tumor-adjacent tissues to systematically dissect the transcriptomic profile of SS in terms of gene expression, alternative splicing, gene fusion, and circular RNAs.Results: A total of 2,309 upregulated and 1,977 downregulated genes were identified between SS and tumor-adjacent tissues. Those upregulated genes could lead to the upregulation of the cell cycle, ribosome, and DNA replication pathways, while the downregulated genes may result in the downregulation of a set of metabolic biological processes and signaling pathways. Moreover, 2,511 genes (including 21 splicing factors) were differentially alternative spliced, indicating that the deregulation of alternative splicing could be one important factor that contributes to tumorigenesis. Additionally, we identified the known gene fusions of SS18-SSX1/SSX2 as well as 11 potentially novel gene fusions. Interestingly, 49 circular RNAs were differentially expressed and their parental genes could function in muscle contraction and muscle system processes.Conclusions: Collectively, our comprehensive dissection of the transcriptomic changes of SS from both transcriptional and post-transcriptional levels provides novel insights into the biology and underlying molecular mechanism of SS.
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Affiliation(s)
- Zhengwang Sun
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Mengchen Yin
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yi Ding
- Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai, China
| | - Zixu Zhu
- No.2 High School of East China Normal University, Shanghai,200000, China
| | - Yangbai Sun
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Kun Li
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wangjun Yan
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
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Acem I, van de Sande MAJ. Prediction tools for the personalized management of soft-tissue sarcomas of the extremity. Bone Joint J 2022; 104-B:1011-1016. [PMID: 36047022 PMCID: PMC9987162 DOI: 10.1302/0301-620x.104b9.bjj-2022-0647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Prediction tools are instruments which are commonly used to estimate the prognosis in oncology and facilitate clinical decision-making in a more personalized manner. Their popularity is shown by the increasing numbers of prediction tools, which have been described in the medical literature. Many of these tools have been shown to be useful in the field of soft-tissue sarcoma of the extremities (eSTS). In this annotation, we aim to provide an overview of the available prediction tools for eSTS, provide an approach for clinicians to evaluate the performance and usefulness of the available tools for their own patients, and discuss their possible applications in the management of patients with an eSTS.Cite this article: Bone Joint J 2022;104-B(9):1011-1016.
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Affiliation(s)
- Ibtissam Acem
- Department of Surgical Oncology and Gastrointestinal Surgery, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.,Department of Orthopaedic Oncology, Leiden University Medical Centre, Leiden, the Netherlands
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Perioperative Adriamycin plus ifosfamide vs. gemcitabine plus docetaxel for high-risk soft tissue sarcomas: randomised, phase II/III study JCOG1306. Br J Cancer 2022; 127:1487-1496. [PMID: 35871234 PMCID: PMC9553903 DOI: 10.1038/s41416-022-01912-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/22/2022] [Accepted: 06/29/2022] [Indexed: 11/09/2022] Open
Abstract
Abstract
Background
This randomised phase II/III trial aimed to determine whether perioperative chemotherapy with gemcitabine plus docetaxel (GD) is non-inferior to the standard Adriamycin plus ifosfamide (AI) in terms of overall survival (OS) in patients with soft tissue sarcoma (STS).
Methods
Patients with localised high-risk STS in the extremities or trunk were randomised to receive AI or GD. The treatments were repeated for three preoperative and two postoperative courses. The primary endpoint was OS.
Results
Among 143 enrolled patients who received AI (70 patients) compared to GD (73 patients), the estimated 3-year OS was 91.4% for AI and 79.2% for GD (hazard ratio 2.55, 95% confidence interval: 0.80–8.14, P = 0.78), exceeding the prespecified non-inferiority margin in the second interim analysis. The estimated 3-year progression-free survival was 79.1% for AI and 59.1% for GD. The most common Grade 3–4 adverse events in the preoperative period were neutropenia (88.4%), anaemia (49.3%), and febrile neutropenia (36.2%) for AI and neutropenia (79.5%) and febrile neutropenia (17.8%) for GD.
Conclusions
Although GD had relatively mild toxicity, the regimen—as administered in this study—should not be considered a standard treatment of perioperative chemotherapy for high-risk STS in the extremities and trunk.
Clinical trial registration
jRCTs031180003.
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49
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Frezza AM, Stacchiotti S, Chibon F, Coindre J, Italiano A, Romagnosa C, Bagué S, Dei Tos AP, Braglia L, Palmerini E, Quagliuolo V, Broto JM, Lopez Pousa A, Grignani G, Brunello A, Blay J, Beveridge RD, Lugowska I, Lesluyes T, Maestro R, Merlo FD, Casali PG, Gronchi A. CINSARC in high-risk soft tissue sarcoma patients treated with neoadjuvant chemotherapy: Results from the ISG-STS 1001 study. Cancer Med 2022; 12:1350-1357. [PMID: 35848358 PMCID: PMC9883440 DOI: 10.1002/cam4.5015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/12/2022] [Accepted: 06/20/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The Complexity INdex in SARComas (CINSARC) is a transcriptional signature derived from the expression of 67 genes involved in mitosis control and chromosome integrity. This study aims to assess CINSARC value of in an independent series of high-risk patients with localized soft tissue sarcoma (STS) treated with preoperative chemotherapy within a prospective, randomized, phase III study (ISG-STS 1001). PATIENTS AND METHODS Patients with available pre-treatment samples, treated with 3 cycles of either standard (ST) preoperative or histotype-tailored (HT) chemotherapy, were scored according to CINSARC (low-risk, C1; high-risk, C2). The 10-year overall survival probability (pr-OS) according to SARCULATOR was calculated, and patients were classified accordingly (low-risk, Sarc-LR, 10-year pr-OS>60%; high-risk, Sarc-HR, 10-year pr-OS<60%). Survival functions were estimated using the Kaplan-Meier method and compared using log-rank test. RESULTS Eighty-six patients were included, 30 C1 and 56 C2, 49 Sarc-LR and 37 Sarc-HR. A low level of agreement between CINSARC and SARCULATOR was observed (Cohen's Kappa = 0.174). The 5-year relapse-free survival in C1 and C2 were 0.57 and 0.55 (p = 0.481); 5-year metastases-free survival 0.63 and 0.64 (p = 0.740); 5-year OS 0.80 and 0.72 (p = 0.460). The 5-year OS in C1 treated with ST and HT chemotherapy was 0.84 and 0.76 (p = 0.251) respectively; in C2 treated it was 0.72 and 0.70 (p = 0.349). The 5-year OS in Sarc-LR treated with S and HT chemotherapy was 0.80 and 0.82 (p = 0.502) respectively; in Sarc-HR it was 0.70 and 0.61 (p = 0.233). CONCLUSIONS Our results, although constrained by the small size of the series, suggest that CINSARC has weak prognostic power in high-risk, localized STS treated with neoadjuvant chemotherapy.
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Affiliation(s)
- Anna Maria Frezza
- Department of Medical OncologyFondazione IRCCS Istituto Nazionale TumoriMilanoItaly
| | - Silvia Stacchiotti
- Department of Medical OncologyFondazione IRCCS Istituto Nazionale TumoriMilanoItaly
| | - Frederic Chibon
- Institut Claudius Régaud, Cancer Research Center of Toulouse (CRCT)IUCT‐ OncopoleToulouseFrance
| | | | - Antoine Italiano
- Early Phase Trials and Sarcoma UnitsInstitut BergoniéBordeauxFrance
| | - Cleofe Romagnosa
- Clinical Genetics and Genetic Counseling ProgramGermans Trias i Pujol HospitalBarcelonaSpain
| | - Silvia Bagué
- Department of PathologyHospital de la Santa Creu i Sant PauBarcelonaSpain
| | | | - Luca Braglia
- Department Infrastructure Research and StatisticsAzienda USL‐IRCCS Reggio EmiliaReggio EmiliaItaly
| | - Emanuela Palmerini
- Osteoncology, Bone and Soft Tissue Sarcomas and Innovative TherapiesIRCCS Istituto Ortopedico RizzoliBolognaItaly
| | - Vittorio Quagliuolo
- Sarcoma, Melanoma and Rare Tumors Surgery UnitIRCCS Humanitas Research HospitalMilanItaly
| | - Javier Martin Broto
- Medical Oncology Department, University Hospital Fundación Jimenez Diaz, Madrid, SpainUniversity Hospital General de Villalba, Madrid, Spain. Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz (IIS/FJD; UAM)MadridSpain
| | - Antonio Lopez Pousa
- Fundacio de Gestio Sanitaria de L'Hospital de la Santa Creu I Sant PauBarcelonaSpain
| | - Giovanni Grignani
- Division of Medical Oncology, Candiolo Cancer InstituteFPO – IRCCSCandioloItaly
| | | | - Jean‐Yves Blay
- Department of Medicine, Centre Leon BerardUNICANCER & University Lyon ILyonFrance
| | | | - Iwona Lugowska
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Centrum OnkologiiInstytut im. Marii Sklodowskiej‐CurieWarsawPoland
| | - Tom Lesluyes
- Institut Claudius Régaud, Cancer Research Center of Toulouse (CRCT)IUCT‐ OncopoleToulouseFrance
| | - Roberta Maestro
- Oncogenetics and Oncogenomics UnitCentro di Riferimento Oncologico di Aviano IRCCSAvianoItaly
| | | | | | - Alessandro Gronchi
- Department of SurgeryFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
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50
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Hettmer S, Linardic CM, Kelsey A, Rudzinski ER, Vokuhl C, Selfe J, Ruhen O, Shern JF, Khan J, Kovach AR, Lupo PJ, Gatz SA, Schäfer BW, Volchenboum S, Minard-Colin V, Koscielniak E, Hawkins DS, Bisogno G, Sparber-Sauer M, Venkatramani R, Merks JHM, Shipley J. Molecular testing of rhabdomyosarcoma in clinical trials to improve risk stratification and outcome: A consensus view from European paediatric Soft tissue sarcoma Study Group, Children's Oncology Group and Cooperative Weichteilsarkom-Studiengruppe. Eur J Cancer 2022; 172:367-386. [PMID: 35839732 DOI: 10.1016/j.ejca.2022.05.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/27/2022] [Accepted: 05/22/2022] [Indexed: 02/07/2023]
Abstract
Rhabdomyosarcomas (RMSs) are the most common soft tissue sarcomas in children/adolescents less than 18 years of age with an annual incidence of 1-2/million. Inter/intra-tumour heterogeneity raise challenges in clinical, pathological and biological research studies. Risk stratification in European and North American clinical trials previously relied on clinico-pathological features, but now, incorporates PAX3/7-FOXO1-fusion gene status in the place of alveolar histology. International working groups propose a coordinated approach through the INternational Soft Tissue SaRcoma ConsorTium to evaluate the specific genetic abnormalities and generate and integrate molecular and clinical data related to patients with RMS across different trial settings. We review relevant data and present a consensus view on what molecular features should be assessed. In particular, we recommend the assessment of the MYOD1-LR122R mutation for risk escalation, as it has been associated with poor outcomes in spindle/sclerosing RMS and rare RMS with classic embryonal histopathology. The prospective analyses of rare fusion genes beyond PAX3/7-FOXO1 will generate new data linked to outcomes and assessment of TP53 mutations and CDK4 amplification may confirm their prognostic value. Pathogenic/likely pathogenic germline variants in TP53 and other cancer predisposition genes should also be assessed. DNA/RNA profiling of tumours at diagnosis/relapse and serial analyses of plasma samples is recommended where possible to validate potential molecular biomarkers, identify new biomarkers and assess how liquid biopsy analyses can have the greatest benefit. Together with the development of new molecularly-derived therapeutic strategies that we review, a synchronised international approach is expected to enhance progress towards improved treatment assignment, management and outcomes for patients with RMS.
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Affiliation(s)
- Simone Hettmer
- Division of Pediatric Hematology and Oncology, Department of Pediatric and Adolescent Medicine, University Medical Center Freiburg, University of Freiburg, Germany
| | - Corinne M Linardic
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA; Department of Pharmacology and Cancer Biology; Duke University of Medicine, Durham, NC, USA
| | - Anna Kelsey
- Department of Paediatric Histopathology, Royal Manchester Children's Hospital, Manchester Foundation Trust, Manchester, UK
| | - Erin R Rudzinski
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Laboratories, Seattle Children's Hospital, Seattle, WA, USA
| | - Christian Vokuhl
- Section of Pediatric Pathology, Department of Pathology, University Hospital Bonn, Germany
| | - Joanna Selfe
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Olivia Ruhen
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Jack F Shern
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA; Pediatric Oncology Branch, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Javed Khan
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Alexander R Kovach
- Department of Pharmacology and Cancer Biology; Duke University of Medicine, Durham, NC, USA
| | - Philip J Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Susanne A Gatz
- Institute of Cancer and Genomic Sciences, Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Birmingham, UK
| | - Beat W Schäfer
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | | | | | - Ewa Koscielniak
- Klinikum der Landeshauptstadt Stuttgart GKAöR, Olgahospital, Stuttgart Cancer Center, Zentrum für Kinder-, Jugend- und Frauenmedizin, Pädiatrie 5 (Pädiatrische Onkologie, Hämatologie, Immunologie), Stuttgart, Germany; Medizinische Fakultät, University of Tübingen, Germany
| | - Douglas S Hawkins
- Seattle Children's Hospital, University of Washington, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Gianni Bisogno
- Hematology Oncology Division, Department of Women's and Children's Health, University of Padova, Padua, Italy
| | - Monika Sparber-Sauer
- Klinikum der Landeshauptstadt Stuttgart GKAöR, Olgahospital, Stuttgart Cancer Center, Zentrum für Kinder-, Jugend- und Frauenmedizin, Pädiatrie 5 (Pädiatrische Onkologie, Hämatologie, Immunologie), Stuttgart, Germany; Medizinische Fakultät, University of Tübingen, Germany
| | - Rajkumar Venkatramani
- Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | | | - Janet Shipley
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK.
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